Sandbox Reserved 335: Difference between revisions

Line 4:

{{STRUCTURE_3cp5 | PDB=3cp5 | SCENE=Sandbox_Reserved_335/Cyt_c/2}}

The '''cytochrome ''c''''' (cyt ''c'') proteins are a superfamily belonging to the class of [http://en.wikipedia.org/wiki/All-α_proteins all-α proteins], which are denoted as such by having an α-helical core. Each protein in this superfamily also contains one or more covalently-bound [http://en.wikipedia.org/wiki/Heme heme prosthetic groups].<ref>PMID:11697912</ref><ref name=main /> The cyt ''c'' superfamily contains many different families, some of which are better characterized than others. These families include monodomain and multi-domain C-type cytochromes, such as [http://proteopedia.org/wiki/index.php/1etp cyt c4], a diheme C-type cytochrome, and [http://proteopedia.org/wiki/index.php/2ozy NrfB], a pentaheme C-type cytochrome. In particular, the monoheme cyt ''c'' from ''Rhodothermus marinus'' has been previously studied and provides an excellent example of how some protein characteristics and structures can be extremely diverse, yet conserved, through evolution.

Line 24:

Line 22:

=== Secondary Structure ===

The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wrap around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix such as helix B' was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main />

The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wrap around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix such as helix B' was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main /> A final thing to note is the number of methionine residues that ''Rm''cyt''c'' contains. In general, cyt ''c'' contains about two methionines whereas ''Rm''cyt''c'' contains seven, located on the lower front side of the heme.<ref name=main />

As determined by X-ray crystallography, the ''Rm''cyt''c'' structure was found to also contain a coordinated sulfate ion; this ion has been seen to mediate crystal contact between neighbouring protein molecules. The carboxylate oxygen of Glu122, when protonated, was also found to be involved in hydrogen bonding with this sulfate ion.<ref name=main />

Sandbox Reserved 335: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 4: / Line 4: @@
 {{STRUCTURE_3cp5 |  PDB=3cp5  |  SCENE=Sandbox_Reserved_335/Cyt_c/2}}
 The '''cytochrome ''c''''' (cyt ''c'') proteins are a superfamily belonging to the class of [http://en.wikipedia.org/wiki/All-α_proteins all-α proteins], which are denoted as such by having an α-helical core. Each protein in this superfamily also contains one or more covalently-bound [http://en.wikipedia.org/wiki/Heme heme prosthetic groups].<ref>PMID:11697912</ref><ref name=main /> The cyt ''c'' superfamily contains many different families, some of which are better characterized than others. These families include monodomain and multi-domain C-type cytochromes, such as [http://proteopedia.org/wiki/index.php/1etp cyt c4], a diheme C-type cytochrome, and [http://proteopedia.org/wiki/index.php/2ozy NrfB], a pentaheme C-type cytochrome. In particular, the monoheme cyt ''c'' from ''Rhodothermus marinus'' has been previously studied and provides an excellent example of how some protein characteristics and structures can be extremely diverse, yet conserved, through evolution.
@@ Line 24: / Line 22: @@
 === Secondary Structure ===
-The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wrap around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix such as helix B' was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main />
+The typical monoheme cyt ''c'' fold is formed by helices <scene name='Sandbox_Reserved_335/Helices/4'>A, C, and E</scene>. ''Rm''cyt''c'' contains seven α-helices that are folded around the heme, all connected by random coils.<ref name=main /> The heme group is axially coordinated by <scene name='Sandbox_Reserved_335/Axial/6'>His49 and Met100</scene>, and the disulfide linkages exist at <scene name='Sandbox_Reserved_335/Cys/1'>Cys45 and Cys48</scene>. The heme group in ''Rm''cyt''c'' is almost completely shielded from solvent due to it being in a mostly hydrophobic pocket. This pocket is formed in part by the seven helices surrounding the ring, but also by two structures that are uncommon in other cytochromes ''c''. First, a 21 amino acid extension of the N-terminal exists, forming <scene name='Sandbox_Reserved_335/Uncommon1/2'>α-helix A' and loop 1</scene>, which wrap around the back of the polypeptide.<ref name=main /> An extension resembling such has only been seen in ''Thermus thermophilus''; however, the extension occurs at the C-terminus rather than the N-terminus.<ref>doi:10.1006/jmbi.1997.1181</ref> A second rarity is that of <scene name='Sandbox_Reserved_335/Uncommon2/2'>helix B'</scene>, inserted between helix D and loop 3, that shields the bottom part of the heme from any solvent.<ref name=main /> In cytochrome ''c''<sub>2</sub> as well as mitochondrial cyt ''c'', a similar yet shorter helix such as helix B' was found, though this helix was present at a different place in the primary sequence. Also, instead of helix B', ''T. thermophilus'' contains a two-stranded [http://en.wikipedia.org/wiki/Beta_sheet β-sheet].<ref name=main /> A final thing to note is the number of methionine residues that ''Rm''cyt''c'' contains. In general, cyt ''c'' contains about two methionines whereas ''Rm''cyt''c'' contains seven, located on the lower front side of the heme.<ref name=main />
 As determined by X-ray crystallography, the ''Rm''cyt''c'' structure was found to also contain a coordinated sulfate ion; this ion has been seen to mediate crystal contact between neighbouring protein molecules. The carboxylate oxygen of Glu122, when protonated, was also found to be involved in hydrogen bonding with this sulfate ion.<ref name=main />