1nqj: Difference between revisions

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OCA

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-[[Image:1nqj.jpg|left|200px]]<br /><applet load="1nqj" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nqj, resolution 1.00&Aring;" />
-'''CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.0 ANGSTROM RESOLUTION IN ABSENCE OF CALCIUM'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.0 ANGSTROM RESOLUTION IN ABSENCE OF CALCIUM==
-The crystal structure of a collagen-binding domain (CBD) with an, N-terminal domain linker from Clostridium histolyticum class I collagenase, was determined at 1.00 A resolution in the absence of calcium (1NQJ) and, at 1.65 A resolution in the presence of calcium (1NQD). The mature enzyme, is composed of four domains: a metalloprotease domain, a spacing domain, and two CBDs. A 12-residue-long linker is found at the N-terminus of each, CBD. In the absence of calcium, the CBD reveals a beta-sheet sandwich fold, with the linker adopting an alpha-helix. The addition of calcium unwinds, the linker and anchors it to the distal side of the sandwich as a new, beta-strand. The conformational change of the linker upon calcium binding, is confirmed by changes in the Stokes and hydrodynamic radii as measured, by size exclusion chromatography and by dynamic light scattering with and, without calcium. Furthermore, extensive mutagenesis of conserved surface, residues and collagen-binding studies allow us to identify the, collagen-binding surface of the protein and propose likely, collagen-protein binding models.
+<StructureSection load='1nqj' size='340' side='right'caption='[[1nqj]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nqj]] is a 2 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=1NQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQJ 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]] 1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=1nqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqj OCA], [https://pdbe.org/1nqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nqj RCSB], [https://www.ebi.ac.uk/pdbsum/1nqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nqj 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nq/1nqj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nqj ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-NQJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_histolyticum Clostridium histolyticum] with CL and LI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Microbial_collagenase Microbial collagenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.3 3.4.24.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NQJ OCA].
+*[[Collagenase 3D structures|Collagenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation., Wilson JJ, Matsushita O, Okabe A, Sakon J, EMBO J. 2003 Apr 15;22(8):1743-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12682007 12682007]
+__TOC__
-[[Category: Clostridium histolyticum]]
+</StructureSection>
-[[Category: Microbial collagenase]]
+[[Category: Hathewaya histolytica]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Matsushita, O.]]
+[[Category: Matsushita O]]
-[[Category: Okabe, A.]]
+[[Category: Okabe A]]
-[[Category: Sakon, J.]]
+[[Category: Sakon J]]
-[[Category: Wilson, J.J.]]
+[[Category: Wilson JJ]]
-[[Category: CL]]
-[[Category: LI]]
-[[Category: beta sandwich]]
-[[Category: chlorine]]
-[[Category: collagen-binding domain]]
-[[Category: lithium]]
-[[Category: metalloprotease]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:35:17 2007''