4ar8: Difference between revisions

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-{{STRUCTURE_4ar8|  PDB=4ar8  |  SCENE=  }}
-===Crystal structure of the peptidase domain of collagenase T from Clostridium tetani complexed with the peptidic inhibitor isoamyl- phosphonyl-Gly-Pro-Ala at 2.05 angstrom resolution.===
-{{ABSTRACT_PUBMED_23703618}}
-==About this Structure==
+==Crystal structure of the peptidase domain of collagenase T from Clostridium tetani complexed with the peptidic inhibitor isoamyl- phosphonyl-Gly-Pro-Ala at 2.05 angstrom resolution.==
-[[4ar8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_tetani Clostridium tetani]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AR8 OCA].
+<StructureSection load='4ar8' size='340' side='right'caption='[[4ar8]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ar8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_tetani Clostridium tetani] 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=4AR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AR8 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]] 2.05&#8491;</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=IP8:ISOPENTENYL+PHOSPHATE'>IP8</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=4ar8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ar8 OCA], [https://pdbe.org/4ar8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ar8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ar8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ar8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COLT_CLOTE COLT_CLOTE] Clostridial collagenases are among the most efficient degraders of eukaryotic collagen known; saprophytes use collagen as a carbon source while pathogens additionally digest collagen to aid in host colonization. Has both tripeptidylcarboxypeptidase on Gly-X-Y and endopeptidase activities; the endopeptidase cuts within the triple helix region of collagen while tripeptidylcarboxypeptidase successively digests the exposed ends, thus clostridial collagenases can digest large sections of collagen (By similarity). The activator domain (residues 57-330) and catalytic subdomain (340-611) open and close around substrate allowing digestion when the protein is closed (PubMed:23703618).[UniProtKB:Q9X721]<ref>PMID:18937627</ref> <ref>PMID:23703618</ref> <ref>PMID:24125730</ref> <ref>PMID:28820255</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Clostridial collagenases are among the most efficient enzymes to degrade by far the most predominant protein in the biosphere. Here we present crystal structures of the peptidases of three clostridial collagenase isoforms (ColG, ColH and ColT). The comparison of unliganded and liganded structures reveal a quaternary subdomain dynamics. In the unliganded ColH structure this globular dynamics is modulated by an aspartate switch motion that binds to the catalytic zinc. We further identified a calcium binding site in proximity to the catalytic zinc. Both ions are required for full activity, explaining why calcium critically affects the enzymatic activity of clostridial collagenases. Our studies further reveal that loops close to the active site thus serve as characteristic substrate selectivity filter. These elements explain the distinct peptidolytic and collagenolytic activities of these enzymes and provide a rational to engineer collagenases with customized substrate specificity as well as for inhibitor design.
-==Reference==
+Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T.,Eckhard U, Schonauer E, Brandstetter H J Biol Chem. 2013 May 23. PMID:23703618<ref>PMID:23703618</ref>
-<ref group="xtra">PMID:023703618</ref><references group="xtra"/><references/>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4ar8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Collagenase 3D structures|Collagenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Clostridium tetani]]
-[[Category: Brandstetter, H.]]
+[[Category: Large Structures]]
-[[Category: Eckhard, U.]]
+[[Category: Synthetic construct]]
-[[Category: Collagenolysis]]
+[[Category: Brandstetter H]]
-[[Category: Hydrolase]]
+[[Category: Eckhard U]]
-[[Category: Hydrolase-inhibitor complex]]
-[[Category: Metalloprotease]]
-[[Category: Peptidase]]