3jqw: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3 at 2 Angstrom resolution in presence of calcium== | ==Crystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3 at 2 Angstrom resolution in presence of calcium== | ||
<StructureSection load='3jqw' size='340' side='right' caption='[[3jqw]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3jqw' size='340' side='right' caption='[[3jqw]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3jqw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3jqw]] is a 3 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=3JQW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JQW 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nqj|1nqj]], [[2o8o|2o8o]], [[3jqu|3jqu]], [[3jqx|3jqx]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nqj|1nqj]], [[2o8o|2o8o]], [[3jqu|3jqu]], [[3jqx|3jqx]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">colH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1498 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">colH ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=3jqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jqw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jqw RCSB], [http://www.ebi.ac.uk/pdbsum/3jqw PDBsum]</span></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=3jqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jqw OCA], [http://pdbe.org/3jqw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jqw RCSB], [http://www.ebi.ac.uk/pdbsum/3jqw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jqw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| Line 17: | Line 18: | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3jqw ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 27: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3jqw" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
| Line 34: | Line 36: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Bacillus histolyticus weinberg and seguin 1916]] | ||
[[Category: Microbial collagenase]] | [[Category: Microbial collagenase]] | ||
[[Category: Bauer, R]] | [[Category: Bauer, R]] | ||
Revision as of 23:20, 9 December 2016
Crystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3 at 2 Angstrom resolution in presence of calciumCrystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3 at 2 Angstrom resolution in presence of calcium
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedClostridium 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||