3wd2: Difference between revisions
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==Serratia marcescens Chitinase B complexed with azide inhibitor== | ==Serratia marcescens Chitinase B complexed with azide inhibitor== | ||
<StructureSection load='3wd2' size='340' side='right' caption='[[3wd2]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='3wd2' size='340' side='right' caption='[[3wd2]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wd2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3wd2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WD2 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1L:[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE'>A1L</scene>, <scene name='pdbligand=DTD:DITHIANE+DIOL'>DTD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1L:[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE'>A1L</scene>, <scene name='pdbligand=DTD:DITHIANE+DIOL'>DTD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wd0|3wd0]], [[3wd1|3wd1]], [[3wd3|3wd3]], [[3wd4|3wd4]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wd0|3wd0]], [[3wd1|3wd1]], [[3wd3|3wd3]], [[3wd4|3wd4]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chiB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chiB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </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=3wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wd2 RCSB], [http://www.ebi.ac.uk/pdbsum/3wd2 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=3wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wd2 OCA], [http://pdbe.org/3wd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wd2 RCSB], [http://www.ebi.ac.uk/pdbsum/3wd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wd2 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 3wd2" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Chitinase]] | [[Category: Chitinase]] | ||
[[Category: Gouda, H]] | [[Category: Gouda, H]] | ||
[[Category: Hirono, S]] | [[Category: Hirono, S]] | ||
Revision as of 02:15, 6 August 2016
Serratia marcescens Chitinase B complexed with azide inhibitorSerratia marcescens Chitinase B complexed with azide inhibitor
Structural highlights
Publication Abstract from PubMedThe Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation. Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor.,Hirose T, Maita N, Gouda H, Koseki J, Yamamoto T, Sugawara A, Nakano H, Hirono S, Shiomi K, Watanabe T, Taniguchi H, Sharpless KB, Omura S, Sunazuka T Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):15892-7. doi:, 10.1073/pnas.1315049110. Epub 2013 Sep 16. PMID:24043811[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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