7wss

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7wss]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Grimontia_hollisae Grimontia hollisae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WSS FirstGlance]. <br>
<table><tr><td colspan='2'>[[7wss]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Grimontia_hollisae Grimontia hollisae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WSS FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7wss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wss OCA], [https://pdbe.org/7wss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wss RCSB], [https://www.ebi.ac.uk/pdbsum/7wss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wss ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7wss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wss OCA], [https://pdbe.org/7wss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wss RCSB], [https://www.ebi.ac.uk/pdbsum/7wss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wss ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/F7IZI6_GRIHO F7IZI6_GRIHO]]
+
[https://www.uniprot.org/uniprot/F7IZI6_GRIHO F7IZI6_GRIHO]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Collagenase from the gram-negative bacterium Grimontia hollisae strain 1706B (Ghcol) degrades collagen more efficiently even than clostridial collagenase, the most widely used industrial collagenase. However, the structural determinants facilitating this efficiency are unclear. Here, we report the crystal structures of ligand-free and Gly-Pro-hydroxyproline (Hyp)-complexed Ghcol at 2.2 and 2.4 A resolution, respectively. These structures revealed that the activator and peptidase domains in Ghcol form a saddle-shaped structure with one zinc ion and four calcium ions. In addition, the activator domain comprises two homologous subdomains, whereas zinc-bound water was observed in the ligand-free Ghcol. In the ligand-complexed Ghcol, we found two Gly-Pro-Hyp molecules, each bind at the active site and at two surfaces on the duplicate subdomains of the activator domain facing the active site, and the nucleophilic water is replaced by the carboxyl oxygen of Hyp at the P1 position. Furthermore, all Gly-Pro-Hyp molecules bound to Ghcol have almost the same conformation as Pro-Pro-Gly motif in model collagen (Pro-Pro-Gly)10, suggesting these three sites contribute to the unwinding of the collagen triple helix. A comparison of activities revealed that Ghcol exhibits broader substrate specificity than clostridial collagenase at the P2 and P2' positions, which may be attributed to the larger space available for substrate binding at the S2 and S2' sites in Ghcol. Analysis of variants of three active-site Tyr residues revealed that mutation of Tyr564 affected catalysis, whereas mutation of Tyr476 or Tyr555 affected substrate recognition. These results provide insights into the substrate specificity and mechanism of G. hollisae collagenase.
+
-
Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen.,Ikeuchi T, Yasumoto M, Takita T, Tanaka K, Kusubata M, Hayashida O, Hattori S, Mizutani K, Mikami B, Yasukawa K J Biol Chem. 2022 Jun 6;298(8):102109. doi: 10.1016/j.jbc.2022.102109. PMID:35679897<ref>PMID:35679897</ref>
+
==See Also==
-
 
+
*[[Collagenase 3D structures|Collagenase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 7wss" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Revision as of 07:23, 3 April 2024

Collagenase from Grimontia (Vibrio) hollisae 1706B

PDB ID 7wss

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7wss"
Personal tools