5fre: Difference between revisions
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<StructureSection load='5fre' size='340' side='right'caption='[[5fre]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='5fre' size='340' side='right'caption='[[5fre]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5fre]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5fre]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FRE FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PG:2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>1PG</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PG:2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>1PG</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5fre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fre OCA], [https://pdbe.org/5fre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fre RCSB], [https://www.ebi.ac.uk/pdbsum/5fre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fre ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0H2YQR1_CLOP1 A0A0H2YQR1_CLOP1] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Clostridium perfringens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Imberty | [[Category: Imberty A]] | ||
[[Category: Mahal | [[Category: Mahal LK]] | ||
[[Category: Pau | [[Category: Pau W]] | ||
[[Category: Pifferi | [[Category: Pifferi C]] | ||
[[Category: Renaudet | [[Category: Renaudet O]] | ||
[[Category: Ribeiro | [[Category: Ribeiro J]] | ||
[[Category: Varrot | [[Category: Varrot A]] | ||
Latest revision as of 16:20, 26 July 2023
Characterization of a novel CBM from Clostridium perfringensCharacterization of a novel CBM from Clostridium perfringens
Structural highlights
FunctionPublication Abstract from PubMedCBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens Glycan arrays revealed its preference towards alpha(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to alpha(2,3)-sialyl-lactose with a Kd of approximately 30 muM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form of the CBM, and using SPR (surface plasmon resonance) we have observed 6-11-fold binding increases due to the avidity affect. The structures of the CBM, resolved by X-ray crystallography, in complex with alpha(2,3)- or alpha(2,6)-sialyl-lactose explain its binding specificity and unusually strong binding. Characterization of a high-affinity sialic acid-specific CBM40 from Clostridium perfringens and engineering of a divalent form.,Ribeiro JP, Pau W, Pifferi C, Renaudet O, Varrot A, Mahal LK, Imberty A Biochem J. 2016 Jul 15;473(14):2109-18. doi: 10.1042/BCJ20160340. Epub 2016 May, 17. PMID:27208171[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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