7xeb: Difference between revisions
New page: '''Unreleased structure''' The entry 7xeb is ON HOLD Authors: Ikeuchi, T., Yasumoto, M., Takita, T., Mizutani, K., Mikami, B., Tanaka, K., Hattori, S., Yasukawa, K. Description: Collag... |
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==Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp== | |||
<StructureSection load='7xeb' size='340' side='right'caption='[[7xeb]], [[Resolution|resolution]] 2.39Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7xeb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Grimontia_hollisae Grimontia hollisae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XEB FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.39Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</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=7xeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xeb OCA], [https://pdbe.org/7xeb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xeb RCSB], [https://www.ebi.ac.uk/pdbsum/7xeb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xeb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7xeb" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Collagenase 3D structures|Collagenase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Yasumoto | </StructureSection> | ||
[[Category: Grimontia hollisae]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Hattori S]] | |||
[[Category: Ikeuchi T]] | |||
[[Category: Mikami B]] | |||
[[Category: Mizutani K]] | |||
[[Category: Takita T]] | |||
[[Category: Tanaka K]] | |||
[[Category: Yasukawa K]] | |||
[[Category: Yasumoto M]] | |||