3itk: Difference between revisions
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<StructureSection load='3itk' size='340' side='right'caption='[[3itk]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='3itk' size='340' side='right'caption='[[3itk]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3itk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3itk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ITK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ITK FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr> | |||
<tr id=' | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3itk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3itk OCA], [https://pdbe.org/3itk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3itk RCSB], [https://www.ebi.ac.uk/pdbsum/3itk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3itk ProSAT]</span></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=3itk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3itk OCA], [https://pdbe.org/3itk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3itk RCSB], [https://www.ebi.ac.uk/pdbsum/3itk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3itk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate. | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arrowsmith CH]] | |||
[[Category: Arrowsmith | [[Category: Bountra C]] | ||
[[Category: Bountra | [[Category: Chaikuad A]] | ||
[[Category: Chaikuad | [[Category: Edwards AM]] | ||
[[Category: Egger S]] | |||
[[Category: Edwards | [[Category: Filippakopoulos P]] | ||
[[Category: Egger | [[Category: Kavanagh KL]] | ||
[[Category: Filippakopoulos | [[Category: Muniz JRC]] | ||
[[Category: Kavanagh | [[Category: Nidetzky B]] | ||
[[Category: Muniz | [[Category: Oppermann U]] | ||
[[Category: Nidetzky | [[Category: Sethi R]] | ||
[[Category: Oppermann | [[Category: Weigelt J]] | ||
[[Category: Yue WW]] | |||
[[Category: Sethi | [[Category: Von Delft F]] | ||
[[Category: Weigelt | |||
[[Category: Yue | |||
[[Category: | |||
Latest revision as of 10:57, 6 September 2023
Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.
Structural highlights
FunctionUGDH_HUMAN Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate. 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 PubMedElevated production of the matrix glycosaminoglycan hyaluronan is strongly implicated in epithelial tumor progression. Inhibition of synthesis of the hyaluronan precursor UDP-glucuronic acid (UDP-GlcUA) therefore presents an emerging target for cancer therapy. Human UDP-glucose 6-dehydrogenase (hUGDH) catalyzes, in two NAD(+)-dependent steps without release of intermediate aldehyde, the biosynthetic oxidation of UDP-glucose (UDP-Glc) to UDP-GlcUA. Here, we present a structural characterization of the hUGDH reaction coordinate using crystal structures of the apoenzyme and ternary complexes of the enzyme bound with UDP-Glc/NADH and UDP-GlcUA/NAD(+). The quaternary structure of hUGDH is a disc-shaped trimer of homodimers whose subunits consist of two discrete alpha/beta domains with the active site located in the interdomain cleft. Ternary complex formation is accompanied by rigid-body and restrained movement of the N-terminal NAD(+) binding domain, sequestering substrate and coenzyme in their reactive positions through interdomain closure. By alternating between conformations in and out of the active site during domain motion, Tyr(14), Glu(161), and Glu(165) participate in control of coenzyme binding and release during 2-fold oxidation. The proposed mechanism of hUGDH involves formation and breakdown of thiohemiacetal and thioester intermediates whereby Cys(276) functions as the catalytic nucleophile. Stopped-flow kinetic data capture the essential deprotonation of Cys(276) in the course of the first oxidation step, allowing the thiolate side chain to act as a trap of the incipient aldehyde. Because thiohemiacetal intermediate accumulates at steady state under physiological reaction conditions, hUGDH inhibition might best explore ligand binding to the NAD(+) binding domain. Structure and mechanism of human UDP-glucose 6-dehydrogenase.,Egger S, Chaikuad A, Kavanagh KL, Oppermann U, Nidetzky B J Biol Chem. 2011 Jul 8;286(27):23877-87. Epub 2011 Apr 18. PMID:21502315[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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