3w6c: Difference between revisions
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== | ==Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharide== | ||
[[3w6c]] is a 4 chain structure with sequence from [ | <StructureSection load='3w6c' size='340' side='right'caption='[[3w6c]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
[[ | == Structural highlights == | ||
[[ | <table><tr><td colspan='2'>[[3w6c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ralstonia_sp._A-471 Ralstonia sp. A-471]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W6C 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]] 2Å</td></tr> | ||
[[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=3w6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w6c OCA], [https://pdbe.org/3w6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w6c RCSB], [https://www.ebi.ac.uk/pdbsum/3w6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w6c ProSAT]</span></td></tr> | |||
[[Category: | </table> | ||
[[Category: | == Function == | ||
[[Category: | [https://www.uniprot.org/uniprot/B7XCV4_9RALS B7XCV4_9RALS] | ||
[[Category: | <div style="background-color:#fffaf0;"> | ||
[[Category: | == Publication Abstract from PubMed == | ||
[[Category: | Chitinase C from Ralstonia sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose-type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptidoglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu-141 acts as a catalytic acid, and that Asp-226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases. | ||
[[Category: | |||
[[Category: | Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis.,Arimori T, Kawamoto N, Shinya S, Okazaki N, Nakazawa M, Miyatake K, Fukamizo T, Ueda M, Tamada T J Biol Chem. 2013 Jun 28;288(26):18696-706. doi: 10.1074/jbc.M113.462135. Epub, 2013 May 8. PMID:23658014<ref>PMID:23658014</ref> | ||
[[Category: | |||
[[Category: | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 3w6c" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Chitinase 3D structures|Chitinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ralstonia sp. A-471]] | |||
[[Category: Arimori T]] | |||
[[Category: Fukamizo T]] | |||
[[Category: Kawamoto N]] | |||
[[Category: Miyatake K]] | |||
[[Category: Nakazawa M]] | |||
[[Category: Okazaki N]] | |||
[[Category: Tamada T]] | |||
[[Category: Ueda M]] | |||
Latest revision as of 15:52, 8 November 2023
Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharideCrystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharide
Structural highlights
FunctionPublication Abstract from PubMedChitinase C from Ralstonia sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose-type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptidoglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu-141 acts as a catalytic acid, and that Asp-226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases. Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis.,Arimori T, Kawamoto N, Shinya S, Okazaki N, Nakazawa M, Miyatake K, Fukamizo T, Ueda M, Tamada T J Biol Chem. 2013 Jun 28;288(26):18696-706. doi: 10.1074/jbc.M113.462135. Epub, 2013 May 8. PMID:23658014[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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