4hpk: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[4hpk]] 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=4HPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HPK FirstGlance]. <br>
-</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.35&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=4hpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hpk OCA], [https://pdbe.org/4hpk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hpk RCSB], [https://www.ebi.ac.uk/pdbsum/4hpk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hpk 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>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Clostridium histolyticum secretes collagenases, ColG and ColH that cause extensive tissue destruction in myonecrosis. The C-terminal collagen-binding domain (CBD) of collagenase is required for insoluble collagen fibril binding and subsequent collagenolysis. The high resolution crystal structures of ColG-CBD (s3b) and ColH-CBD (s3) are reported in this paper. The new X-ray structure of s3 was solved at 2.0 A resolution (R=17.4%, R(free)=23.3%), while the resolution of the previously determined s3b was extended to 1.4 A (R=17.9%, R(free)=21.0%). Despite sharing only 30% sequence identity, the molecules resemble one another closely (r.m.s.d. C(alpha) = 1.5 A). All but one residue whose sidechain chelates with Ca(2+) are conserved. The dual Ca(2+) binding site in s3 is completed by an unconserved aspartate. Differential scanning calorimetric measurements showed that s3 gains thermal stability, comparable to s3b, by binding to Ca(2+) (holo T(M)=94.1 degrees C, apo T(M)=70.2 degrees C). Holo s3 is also stabilized against chemical denaturants, urea and guanidine HCl. The three most critical residues for collagen interaction in s3b are conserved in s3. The general shape of the binding pocket is retained by altered loop structures and side chain positions. Small angle X-ray scattering data revealed that s3 also binds asymmetrically to mini-collagen. Besides the calcium-binding sites and the collagen-binding pocket, architecturally important hydrophobic residues and hydrogen-bonding network around the cis-peptide bond are well-conserved within metallopeptidase subfamily M9B. CBDs were previously shown to bind to extracellular matrix of various tissues. Compactness and extreme stability in physiological Ca(2+) concentration possibly make both CBDs suitable for targeted growth factor delivery.
-Structural comparison of ColH and ColG collagen-binding domains from Clostridium histolyticum.,Bauer R, Wilson JJ, Philominathan ST, Davis D, Matsushita O, Sakon J J Bacteriol. 2012 Nov 9. PMID:23144249<ref>PMID:23144249</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4hpk" style="background-color:#fffaf0;"></div>
 ==See Also==