Sandbox Reserved 1125: Difference between revisions

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===== Zn998 : the structural zinc =====

The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/1'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref>PMID:8137810</ref>

One of them is as well bound to the Glu residue thanks to a hydrogen bond. At first, the Gly 206 residue of the substrate binds the active site thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part. Then, the Ala 182 residue of the enzyme makes a hydrogen bond with the NH group of the substrate: this allows the substrate to enter the cavity of the catalytic site. The rest of the protein is stabilized by 4 hydrogen bonds with the amino acid located in the cavity.

<font color='red'>The conserved cysteine present in the cysteine-switch motif (89-96) binds the catalytic zinc ion, thus inhibiting the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme.</font>

=== Hinge domain ===

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MMP-8 is secreted as inactive proproteins and then activated after a cleavage by extracellular proteinases. Indeed, it can't be activated without removal of the activation peptide. But recent evidences suggest that this protease activation is blocked by the formation of an intramolecular complex between the propeptide domain on the Cysteine residue (Cys91) and essential zinc atom in the catalytic domain. It is called the ''Cysteine-switch''. This discovery is unprecedented in enzymology and offers the opportunity for multiple modes of physiological activation of MMP-8. Moreover, since conditions in different cells and tissues may match those necessary to effect one of these activation modes for a given MMP, this may offer metabolic flexibility in the control of MMP activation.<ref>PMID:2164689</ref>

To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains. The linker peptide can position the hemopexin domain in such a way that it bends over the active site of the catalytic domain. But understanding how the Hemopexin domain assists in the cleavage of collagen is elusive.<ref>PMID:15257288</ref> Thus, the collagen would be captured between these two domains. However, the active site cannot accommodate the entire triple helix in a native state. The linker peptide would, by means of its collagen-like conformation, change the quaternary structure of the captured collagen. Interactions between proline residues of the collagenase and a specific region of the collagen would generate a “proline zipper,” resulting in destabilization of the cleavage site area of the collagen. After destabilization, one chain of the triple helix fits in the <scene name='71/719866/Catalytic_site/4'>active site</scene> of ~~MMP-8~~ and the ~~carbonyl group of the peptide bond coordinates with it~~.<ref>PMID:17185359</ref> ~~This displaces the water molecule from the zinc atom.~~ The ~~peptide hydrolysis is assisted by the~~ carboxyl group of the glutamate~~, which~~ serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. ~~A pocket to~~ the ~~right~~ of the ~~active-site zinc, called~~ the ~~specificity pocket or <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>, accommodates the side chain~~ of the substrate ~~residue~~, ~~which~~ becomes the new N-terminus after cleavage~~. The sizes of the S1′ pocket vary among the MMPs, and this is one of the major determining factors of substrate specificity~~.<ref>PMID:12730128</ref>

To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains. The linker peptide can position the hemopexin domain in such a way that it bends over the active site of the catalytic domain. But understanding how the Hemopexin domain assists in the cleavage of collagen is elusive.<ref>PMID:15257288</ref> Thus, the collagen would be captured between these two domains. However, the active site cannot accommodate the entire triple helix in a native state. The linker peptide would, by means of its collagen-like conformation, change the quaternary structure of the captured collagen. Interactions between proline residues of the collagenase and a specific region of the collagen would generate a “proline zipper,” resulting in destabilization of the cleavage site area of the collagen. After destabilization, one chain of the triple helix fits in the specificity pocket or <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene> to the right of the active-site zinc. At first, the Gly residue of the substrate binds the <scene name='71/719866/Catalytic_site/4'>active site</scene> thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part.<ref>PMID:17185359</ref> The carboxyl group of the glutamate serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. Then, the Alanine residue of the enzyme makes a hydrogen bond with the NH group of the substrate. Moreover, this NH group becomes the new N-terminus after cleavage.<ref>PMID:12730128</ref>

The cleavage is at Gly775–Ile776 or Leu776 in each alpha-chain of the collagen molecule<ref>PMID:9094424</ref> and takes place at neutral pH. It generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases.<ref>[http://www.ebi.ac.uk/interpro/entry/IPR028709 "Neutrophil collagenase"]</ref>

The cleavage is at Gly775–Ile776 or Leu776 in each alpha-chain of the collagen molecule.<ref>PMID:9094424</ref> ~~The cleavage, taking~~ place at neutral pH, generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases.<ref>[http://www.ebi.ac.uk/interpro/entry/IPR028709 "Neutrophil collagenase"]</ref>

== Regulation by inhibitors ==

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Line 78:

Overexpression of MMP-8, or inadequate control by TIMPs, can be associated with a lot of pathological conditions: psoriasis, sclerosis, osteoarthritis, rheumatoid arthritis, osteoporosis, Alzheimer's disease, tumor growh and metastasis.<ref>[http://www.enzim.hu/~lbarna/articles/19173605.pdf "Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S1′ Subsite of Matrix Metalloproteinase 8"]</ref>

Neutrophil collagenase or collagenase 2 (MMP-8) is unique among the family of matrix metalloproteinases (MMPs) because of its exclusive pattern of expression in inflammatory conditions.<ref>PMID:9727011</ref>

~~== Relevance ==~~

~~== Structural highlights ==~~

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

Sandbox Reserved 1125: Difference between revisions

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@@ Line 44: / Line 44: @@
 ===== Zn998 : the structural zinc =====
 The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/1'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref>PMID:8137810</ref>
-One of them is as well bound to the Glu residue thanks to a hydrogen bond. At first, the Gly 206 residue of the substrate binds the active site thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part. Then, the Ala 182 residue of the enzyme makes a hydrogen bond with the NH group of the substrate: this allows the substrate to enter the cavity of the catalytic site. The rest of the protein is stabilized by 4 hydrogen bonds with the amino acid located in the cavity.
-<font color='red'>The conserved cysteine present in the cysteine-switch motif (89-96) binds the catalytic zinc ion, thus inhibiting the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme.</font>
 === Hinge domain ===
@@ Line 66: / Line 62: @@
 MMP-8 is secreted as inactive proproteins and then activated after a cleavage by extracellular proteinases. Indeed, it can't be activated without removal of the activation peptide. But recent evidences suggest that this protease activation is blocked by the formation of an intramolecular complex between the propeptide domain on the Cysteine residue (Cys91) and essential zinc atom in the catalytic domain. It is called the ''Cysteine-switch''. This discovery is unprecedented in enzymology and offers the opportunity for multiple modes of physiological activation of MMP-8. Moreover, since conditions in different cells and tissues may match those necessary to effect one of these activation modes for a given MMP, this may offer metabolic flexibility in the control of MMP activation.<ref>PMID:2164689</ref>
-To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains. The linker peptide can position the hemopexin domain in such a way that it bends over the active site of the catalytic domain. But understanding how the Hemopexin domain assists in the cleavage of collagen is elusive.<ref>PMID:15257288</ref> Thus, the collagen would be captured between these two domains. However, the active site cannot accommodate the entire triple helix in a native state. The linker peptide would, by means of its collagen-like conformation, change the quaternary structure of the captured collagen. Interactions between proline residues of the collagenase and a specific region of the collagen would generate a “proline zipper,” resulting in destabilization of the cleavage site area of the collagen. After destabilization, one chain of the triple helix fits in the <scene name='71/719866/Catalytic_site/4'>active site</scene> of MMP-8 and the carbonyl group of the peptide bond coordinates with it.<ref>PMID:17185359</ref> This displaces the water molecule from the zinc atom. The peptide hydrolysis is assisted by the carboxyl group of the glutamate, which serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. A pocket to the right of the active-site zinc, called the specificity pocket or <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>, accommodates the side chain of the substrate residue, which becomes the new N-terminus after cleavage. The sizes of the S1′ pocket vary among the MMPs, and this is one of the major determining factors of substrate specificity.<ref>PMID:12730128</ref>
+To express collagenolytic activity, MMP-8 needs to have both the catalytic and hemopexin domains. The linker peptide can position the hemopexin domain in such a way that it bends over the active site of the catalytic domain. But understanding how the Hemopexin domain assists in the cleavage of collagen is elusive.<ref>PMID:15257288</ref> Thus, the collagen would be captured between these two domains. However, the active site cannot accommodate the entire triple helix in a native state. The linker peptide would, by means of its collagen-like conformation, change the quaternary structure of the captured collagen. Interactions between proline residues of the collagenase and a specific region of the collagen would generate a “proline zipper,” resulting in destabilization of the cleavage site area of the collagen. After destabilization, one chain of the triple helix fits in the specificity pocket or <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene> to the right of the active-site zinc. At first, the Gly residue of the substrate binds the <scene name='71/719866/Catalytic_site/4'>active site</scene> thanks to the Zn2+ atom. When it binds it takes the place of unstable water molecules and establishes stabilizing interactions with the active site thanks to its C terminal part.<ref>PMID:17185359</ref> The carboxyl group of the glutamate serves as a general base to draw a proton from the displaced water molecule, thereby facilitating the nucleophilic attack of the water molecule on the carbonyl carbon of the peptide scissile bond. Then, the Alanine residue of the enzyme makes a hydrogen bond with the NH group of the substrate. Moreover, this NH group becomes the new N-terminus after cleavage.<ref>PMID:12730128</ref>
+The cleavage is at Gly775–Ile776 or Leu776 in each alpha-chain of the collagen molecule<ref>PMID:9094424</ref> and takes place at neutral pH. It generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases.<ref>[http://www.ebi.ac.uk/interpro/entry/IPR028709 "Neutrophil collagenase"]</ref>
-The cleavage is at Gly775–Ile776 or Leu776 in each alpha-chain of the collagen molecule.<ref>PMID:9094424</ref> The cleavage, taking place at neutral pH, generates fragments that spontaneously lose their helical conformation, denature to gelatin, and become soluble. The gelatin is then susceptible to attack by gelatinases and other proteases.<ref>[http://www.ebi.ac.uk/interpro/entry/IPR028709 "Neutrophil collagenase"]</ref>
 == Regulation by inhibitors ==
@@ Line 83: / Line 78: @@
 Overexpression of MMP-8, or inadequate control by TIMPs, can be associated with a lot of pathological conditions: psoriasis, sclerosis, osteoarthritis, rheumatoid arthritis, osteoporosis, Alzheimer's disease, tumor growh and metastasis.<ref>[http://www.enzim.hu/~lbarna/articles/19173605.pdf "Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S1′ Subsite of Matrix Metalloproteinase 8"]</ref>
 Neutrophil collagenase or collagenase 2 (MMP-8) is unique among the family of matrix metalloproteinases (MMPs) because of its exclusive pattern of expression in inflammatory conditions.<ref>PMID:9727011</ref>
-== Relevance ==
-== Structural highlights ==
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
 </StructureSection>