5iku: Difference between revisions

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-==Crystal structure of the Clostridium histolyticum ColG tandem collagen-binding domain s3as3b in the presence of calcium at 1.9 Angstrom resolution==
+==Crystal structure of the Hathewaya histolytica ColG tandem collagen-binding domain s3as3b in the presence of calcium at 1.9 Angstrom resolution==
-<StructureSection load='5iku' size='340' side='right' caption='[[5iku]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='5iku' size='340' side='right'caption='[[5iku]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5iku]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_histolyticus"_weinberg_and_seguin_1916 "bacillus histolyticus" weinberg and seguin 1916]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5iku]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hathewaya_histolytica Hathewaya histolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IKU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">colG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1498 "Bacillus histolyticus" Weinberg and Seguin 1916])</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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5iku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iku OCA], [http://pdbe.org/5iku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iku RCSB], [http://www.ebi.ac.uk/pdbsum/5iku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iku 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=5iku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iku OCA], [https://pdbe.org/5iku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iku RCSB], [https://www.ebi.ac.uk/pdbsum/5iku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iku ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/COLG_HATHI COLG_HATHI] 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 (PubMed:3002446). Active on soluble type I collagen, insoluble collagen, azocoll, soluble PZ-peptide (all collagenase substrates) and gelatin (PubMed:9922257). The full-length protein has collagenase activity, while the in vivo derived C-terminally truncated shorter versions only act on gelatin (PubMed:9922257). In vitro digestion of soluble calf skin collagen fibrils requires both ColG and ColH; ColG forms missing the second collagen-binding domain are also synergistic with ColH, although their overall efficiency is decreased (PubMed:18374061, PubMed:22099748). The activator domain (residues 119-388) and catalytic subdomain (389-670) open and close around substrate using a Gly-rich hinge (387-397), allowing digestion when the protein is closed (PubMed:21947205, PubMed:23703618). Binding of collagen requires Ca(2+) and is inhibited by EGTA; the collagen-binding domain (CBD, S3a plus S3b) specifically recognizes the triple-helical conformation made by 3 collagen protein chains in the triple-helical region (PubMed:11121400). Isolated CBD (S3a plus S3b) binds collagen fibrils and sheets of many tissues (PubMed:11913772).<ref>PMID:11121400</ref> <ref>PMID:11913772</ref> <ref>PMID:18374061</ref> <ref>PMID:18937627</ref> <ref>PMID:21947205</ref> <ref>PMID:22099748</ref> <ref>PMID:23703618</ref> <ref>PMID:24125730</ref> <ref>PMID:28820255</ref> <ref>PMID:3002446</ref> <ref>PMID:9922257</ref>
+==See Also==
+*[[Collagenase 3D structures|Collagenase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus histolyticus weinberg and seguin 1916]]
+[[Category: Hathewaya histolytica]]
-[[Category: Bauer, R]]
+[[Category: Large Structures]]
-[[Category: Janowska, K]]
+[[Category: Bauer R]]
-[[Category: Matsushita, O]]
+[[Category: Janowska K]]
-[[Category: Roeser, R]]
+[[Category: Matsushita O]]
-[[Category: Sakon, J]]
+[[Category: Roeser R]]
-[[Category: Calcium-binding protein collagen-binding protein]]
+[[Category: Sakon J]]
-[[Category: Protein binding]]