https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Randi+WoodbeckProteopedia - User contributions [en]2026-09-26T04:43:41ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064811Sonic Hedgehog2010-04-01T04:25:20Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. Mutations in the ''Shh'' gene can also result in severe developmental consequences, including [http://en.wikipedia.org/wiki/Holoprosencephaly holoprosencephaly] <ref>PMID: 8896572</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and yellow, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the [http://en.wikipedia.org/wiki/Floor_plate floor plate] within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
=References=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064422Sonic Hedgehog2010-03-31T17:13:03Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. Mutations in the ''Shh'' gene can also result in severe developmental consequences, including [http://en.wikipedia.org/wiki/Holoprosencephaly holoprosencephaly] <ref>PMID: 8896572</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and yellow, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
=References=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064420Sonic Hedgehog2010-03-31T17:12:25Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. Mutations in the ''Shh'' gene can also result in severe developmental consequences, including [http://en.wikipedia.org/wiki/Holoprosencephaly holoprosencephaly] <ref>PMID: 8896572</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and yellow, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064419Sonic Hedgehog2010-03-31T17:10:48Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. Mutations in the ''Shh'' gene can also result in severe developmental consequences, including [http://en.wikipedia.org/wiki/Holoprosencephaly holoprosencephaly] <ref>PMID: 8896572</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and white, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064415Sonic Hedgehog2010-03-31T17:05:57Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. Mutations in the ''Shh'' gene can also result in severe developmental consequences, including [http://en.wikipedia.org/wiki/Holoprosencephaly holoprosencephaly]. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and white, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064410Sonic Hedgehog2010-03-31T16:59:49Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, shown in red and white, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064361Sonic Hedgehog2010-03-31T15:11:47Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="Palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064358Sonic Hedgehog2010-03-31T15:06:14Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds [http://en.wikipedia.org/wiki/Heparin heparin], this interaction is believed to comprise a heparin-binding region<ref name="palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064357Sonic Hedgehog2010-03-31T15:03:20Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds heparin, this interaction is believed to comprise a heparin-binding region<ref name="palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1064356Sonic Hedgehog2010-03-31T15:02:27Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N also contains a single sulphate molecule, which interacts with arginine residues at the interface of two Shh-N molecules. Since Shh-N binds heparin, this interaction is believed to comprise a heparin-binding region<ref name="palm"/>. <br />
<br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1063017Sonic Hedgehog2010-03-31T09:48:00Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref name="process">PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning<ref name="process"/>, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062990Sonic Hedgehog2010-03-31T09:45:47Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling (Figure 2)<ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062967Sonic Hedgehog2010-03-31T09:43:09Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. [Note: This figure is adapted from references <ref name="Palm"/> and <ref name="signal"/>.] ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062948Sonic Hedgehog2010-03-31T09:40:18Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis<ref name="Palm"/><ref name="signal"/>. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube<ref>PMID: 8223247</ref>. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062923Sonic Hedgehog2010-03-31T09:34:43Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis<ref name="Palm"/><ref name="signal"/>. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062922Sonic Hedgehog2010-03-31T09:33:29Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref name="limb">PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis <ref name="signal"/>. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning <ref name="limb"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062916Sonic Hedgehog2010-03-31T09:32:15Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref name="neuron">PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis <ref name="signal"/>. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphogen to establish somite patterning, motor neuron formation in the neural tube<ref name="neuron"/>, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062882Sonic Hedgehog2010-03-31T09:29:21Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N is released from the cell membrane for long-range signaling by zinc-dependent proteolysis <ref name="signal"/>. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref name="signal">PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062858Sonic Hedgehog2010-03-31T09:25:25Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image: Short and Long-Range.jpg | thumb | '''Figure 2.''' Shh-N (pink) is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. ]]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062846Sonic Hedgehog2010-03-31T09:23:34Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image:Short and Long-Range.jpg |thumb| '''Figure 2.''' Shh-N (pink) is released from the cell membrane for long-range signaling by zinc-dependent proteolysis.]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062837Sonic Hedgehog2010-03-31T09:21:46Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
[[Image:Short and Long-Range.jpg] thumb| '''Figure 2.''' Shh-N (pink) is released from the cell membrane for long-range signaling by zinc-dependent proteolysis. ]The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 3.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 3)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 3) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=File:Short_and_Long-Range.jpg&diff=1062804File:Short and Long-Range.jpg2010-03-31T09:15:28Z<p>Randi Woodbeck: Short and long-range signaling activity of Shh.</p>
<hr />
<div>Short and long-range signaling activity of Shh.</div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062798Sonic Hedgehog2010-03-31T09:13:30Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg |left| thumb| '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]] In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062787Sonic Hedgehog2010-03-31T08:26:32Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
[[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062786Sonic Hedgehog2010-03-31T08:24:07Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene> (Figure 1). [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062785Sonic Hedgehog2010-03-31T08:20:59Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling occurs in a contact-dependent fashion and is associated with induction of the floor plate within the neural tube. During long-range signaling, Shh-N acts as a morphonen to establish somite patterning, motor neuron formation in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062784Sonic Hedgehog2010-03-31T08:12:27Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected autoproteolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling is associated with induction of the floor plate within the neural tube, while long-range signaling is associated with somite patterning, the establishment of motor neurons in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062782Sonic Hedgehog2010-03-31T08:07:03Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood<ref name="papinsky"/>. Short-range signaling is associated with induction of the floor plate within the neural tube, while long-range signaling is associated with somite patterning, the establishment of motor neurons in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062780Sonic Hedgehog2010-03-31T08:05:06Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood. Short-range signaling is associated with induction of the floor plate within the neural tube, while long-range signaling is associated with somite patterning, the establishment of motor neurons in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2)<ref name="ShhGli"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062779Sonic Hedgehog2010-03-31T08:02:54Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood. Short-range signaling is associated with induction of the floor plate within the neural tube, while long-range signaling is associated with somite patterning, the establishment of motor neurons in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a 12 transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2) <ref name="Path"/>. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062778Sonic Hedgehog2010-03-31T07:55:51Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N are also likely, including an Shh receptor or other types of signaling molecules involved in the Shh pathway. Whichever the substrate, the discovery of a potential proteolytic activity for Shh-N seems to provide a mechanism for regulating short-range and long-range signaling, which until now has been poorly understood. Short-range signaling is associated with induction of the floor plate within the neural tube, while long-range signaling is associated with somite patterning, the establishment of motor neurons in the neural tube, and anteroposterior limb patterning. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2). When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062769Sonic Hedgehog2010-03-31T07:31:18Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other kinds of signaling molecules involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' The Sonic hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2). When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062768Sonic Hedgehog2010-03-31T07:30:00Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other kinds of signaling molecules involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle (Figure 2). When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes (Figure 2) <ref name="ShhGli"/>. <br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062767Sonic Hedgehog2010-03-31T07:25:55Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref name="papinsky">PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N <ref name="papinsky"/>. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062762Sonic Hedgehog2010-03-31T07:15:01Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as the anterioposterior patterning of vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062758Sonic Hedgehog2010-03-31T07:07:05Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
= Introduction =<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
= Biosynthesis =<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
= Structural Overview =<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
= Function = <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062755Sonic Hedgehog2010-03-31T07:02:35Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>. The suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062753Sonic Hedgehog2010-03-31T06:59:29Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''SONIC HEDGEHOG'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and the suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062752Sonic Hedgehog2010-03-31T06:56:26Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
'''Sonic Hedgehog'''<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and the suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062737Sonic Hedgehog2010-03-31T05:54:31Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
The crystal structure of Shh-N contains a single sulphate molecule. <br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and the suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062723Sonic Hedgehog2010-03-31T05:31:36Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, three non-coordinating residues in Shh-N (<scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene>) are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and the suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062719Sonic Hedgehog2010-03-31T05:28:31Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and the suspected hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. However, other possible substrates for Shh-N proteolysis are also likely, including an Shh receptor or other signaling proteins involved in the Shh pathway. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062702Sonic Hedgehog2010-03-31T05:03:22Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule<ref name="Palm"/>.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062701Sonic Hedgehog2010-03-31T04:57:29Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | '''Figure 2.''' Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062700Sonic Hedgehog2010-03-31T04:56:02Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | '''Figure 1.''' A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | Figure 2. Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062699Sonic Hedgehog2010-03-31T04:54:54Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. [[Image:Catalytic site.png |left| thumb | Figure 1. A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å, respectively. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule.]] Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | Figure 2. Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062694Sonic Hedgehog2010-03-31T04:43:05Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. [[Image:Catalytic site.png | align='left' | size='300' | Figure 1. A close-up of the zinc coordination site of Shh-N, showing His 141, Asp 148, and His 183 separated by distances of 2.06, 1.97, and 2.08 Å. The zinc-bound water molecule is also shown in line with Glu 177, which is thought to participate in hydrolysis by abstracting a proton from the water molecule.]] <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | Figure 2. Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=File:Catalytic_site.png&diff=1062688File:Catalytic site.png2010-03-31T04:33:47Z<p>Randi Woodbeck: A closer look at the zinc coordination site of Shh-N.</p>
<hr />
<div>A closer look at the zinc coordination site of Shh-N.</div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Sonic_Hedgehog&diff=1062682Sonic Hedgehog2010-03-31T04:28:34Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
<br />
= '''Sonic Hedgehog''' =<br />
{{STRUCTURE_1vhh | PDB=1vhh | SCENE=Sandbox_191/Scenedefault/4}}<br />
== Introduction ==<br />
<br />
Sonic hedgehog (Shh) is a member of the Hedgehog (Hh) family of secreted extracellular signaling proteins, which serve important roles in regulating both short-range and long-range patterning processes in developing invertebrate and vertebrate tissues<ref>PMID: 7867057</ref>. First discovered in ''Drosophila'', where mutations of the single ''Hedgehog'' gene produces larvae that are covered in hedgehog-like denticles, Hh proteins are encoded by at least three genes in mammals - ''Sonic'', ''Desert'', and ''Indian hedgehog''<ref>PMID: 7916661</ref>. With the ability to control such fundamental processes as pattern formation in vertebrate limb buds<ref>PMID: 8269518</ref>, the formation of motor neurons in the neural tube <ref>PMID: 7736596</ref>, and the development and maintenance of tissues and organs<ref>PMID: 10980429</ref>, Shh is the most well-studied member of the Hh signaling proteins<ref>PMID: 10753901</ref>. Excessive signaling in adult cells has been implicated in the development of several human cancers<ref>PMID: 14737121</ref><ref name="Path">PMID: 12044012</ref>. <br />
<br />
== Biosynthesis ==<br />
<br />
As with all members of the Hh family, Shh biosynthesis begins with an unusual molecular processing event. Following cleavage of its signal peptide, the Shh precursor protein is autocatalytically cleaved into two functionally distinct domains, a 19-kDa amino-terminal domain (Shh-N) and a 27-kDa carboxy-terminal domain (Shh-C)<ref>PMID: 7891723</ref>. Spanning residues 24 to 197 in human Shh, Shh-N is responsible for all of the local and long-range signaling activities of Shh. Shh-C possesses an intramolecular transferase activity responsible for covalent attachment of a molecule of cholesterol to the C-terminus of Shh-N. The addition of cholesterol serves to tether Shh-N to the cell membrane, restricting its range of activity to that of local signaling only<ref>PMID: 8824192</ref>. A second modification involving the attachment of a palmitoyl group to Cys-24 on the protein's N-terminus has recently been discovered in insect and mammalian cells. This N-terminal modification is thought to increase the potency of the Shh-N signal as much as 30-fold<ref>PMID: 9593755</ref>. <br />
<br />
== Structural Overview ==<br />
<br />
The three-dimensional structure of murine Shh-N (residues 39-195) is shown as 1VHH. An α + β sandwich consisting of two <scene name='Sandbox_191/Scene2/5'> α-helices</scene> and a six-stranded, mixed <scene name='Sandbox_191/Scene3/5'> β-sheet</scene> makes up the core of the structure, along with a two-stranded, antiparallel β-sheet<ref name="Palm"/>. Although this type of folding arrangement has not yet been seen in other proteins, the presence of a <scene name='Sandbox_191/Scene4/3'>tetrahedrally coordinated zinc ion</scene> in Shh-N bears close structural resemblance to the zinc coordination sites of zinc hydrolases, including thermolysin and carboxypeptidase A. Three amino acid side chains – <scene name='Sandbox_191/Scene4/4'>His 141, Asp 148, and His 183</scene> – are bound to the zinc ion in the crystal structure, along with a single <scene name='Sandbox_191/Scene4/5'>molecule of water</scene>. Zinc ions that serve a structural role in proteins are normally coordinated by four amino acid side chains and are not usually exposed to the surrounding solvent. The presence of a zinc-bound water molecule in Shh-N, by contrast, is indicative of a catalytic function. In zinc hydrolases, the water molecule is key to the protein's enzymatic activity when its proton is removed by a nearby glutamate residue. <scene name='Sandbox_191/Scene4/6'>Glu 177</scene> (Figure 1) likely serves the same role in Shh-N, further supporting a novel, hydrolytic function for this protein. Based on the catalytic mechanisms for thermolysin and carboxypeptidase A, <scene name='Sandbox_191/Scene4/7'>His 135, His 181, and Glu 127</scene> in Shh-N are also believed to participate in a potential hydrolysis reaction<ref name="Palm">PMID: 7477329</ref>. <br />
<br />
== Function == <br />
<br />
The tetrahedrally coordinated zinc ion of Shh-N, along with the non-coordinating residues thought to assist hydrolysis, are highly conserved among vertebrate Hh proteins. A potential hydrolytic activity is therefore expected to play an important cellular role. In pursuit of a substrate for Shh-N, it was found that <scene name='Sandbox_191/Scene3/6'>Ala 194 and Lys 195</scene> near the C-terminus of one Shh-N molecule can hydrogen bond with residues in the zinc binding site of a second Shh-N molecule. This indicates that the protein may be capable of cleaving between Lys 195 and Ser 196 within its own C-terminus <ref name="Palm"/>. This is the most highly conserved region of Hh proteins<ref>PMID: 8807822</ref>, and a possible hydrolytic function of Shh-N has been suggested to liberate the tethered protein from the cell membrane to facilitate long-range signaling <ref name="Palm"/>. <br />
<br />
== Sonic Signaling: The Shh-Gli Pathway ==<br />
<br />
[[Image: SHH SIGNALING PATHWAY.jpg | thumb | Sonic Hedgehog signaling pathway. In the absence of Shh, Patched inhibits Smo. Inhibition of Patched by Shh activates normal developmental processes. [Note: This figure is adapted from references <ref name="Path"/> and <ref name="ShhGli">PMID: 16339192</ref>.] ]]<br />
<br />
In the absence of a Shh signal, a transmembrane receptor protein called Patched blocks the function of Smoothened (Smo), a seven-pass transmembrane protein, by keeping it sequestered in an intracellular vesicle. When Shh binds to Patched, inhibition of Smo by Patched is relieved. Patched becomes endocytosed, and Smo translocates to the cell surface. In vertebrates, Smo localizes to the surface of the primary cilium, initiating a signaling cascade that leads to the activation of Gli transcription factors <ref name="Path"/>. Present in both the nucleus and cytoplasm, there are three of these regulatory proteins (''Gli1'', ''Gli2'', and ''Gli3''). Following Shh signaling, all three proteins can act as transcriptional activators of Shh target genes. Gli3, however, can act as both an activator and repressor; in the absence of Shh signaling, Gli3 is cleaved by the proteasome, and its truncated form accumulates in the nucleus where it represses transcription of Shh-responsive genes <ref name="ShhGli"/>. <br />
<br />
== Mutations ==<br />
<br />
='''References'''=<br />
<references/></div>Randi Woodbeckhttps://proteopedia.org/index.php?title=Amylase&diff=1062657Amylase2010-03-31T03:58:01Z<p>Randi Woodbeck: </p>
<hr />
<div><table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr><br />
Shane Riley<br />
<br />
----<br />
<br />
<br />
{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}<br />
<br />
='''α-Amylase'''=<br />
=Introduction=<br />
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.<br />
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=Structure=<br />
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca<sup>2+</sup>-Na<sup>+</sup>-Ca<sup>2+</sup>. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca<sup>2+</sup> binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.<br />
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca<sup>2+</sup> ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.<br />
==Chloride Dependent Enzymes==<br />
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.<br />
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=Function=<br />
==Mechanism==<br />
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>. <br />
==Human Salivary and Pancreatic α-Amylase==<br />
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway. <br />
==Regulation==<br />
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.<br />
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=Industrial Uses=<br />
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains. <br />
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=References=<br />
<references/></div>Randi Woodbeck