4a7x: Difference between revisions
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==Crystal structure of uridylate kinase from Helicobacter pylori== | ==Crystal structure of uridylate kinase from Helicobacter pylori== | ||
<StructureSection load='4a7x' size='340' side='right' caption='[[4a7x]], [[Resolution|resolution]] 2.49Å' scene=''> | <StructureSection load='4a7x' size='340' side='right'caption='[[4a7x]], [[Resolution|resolution]] 2.49Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4a7x]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4a7x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A7X FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.49Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr> | |||
<tr><td class="sblockLbl"><b> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4a7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a7x OCA], [https://pdbe.org/4a7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a7x RCSB], [https://www.ebi.ac.uk/pdbsum/4a7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a7x ProSAT]</span></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </table> | ||
<table> | == Function == | ||
[https://www.uniprot.org/uniprot/PYRH_HELPY PYRH_HELPY] Catalyzes the reversible phosphorylation of UMP to UDP.[HAMAP-Rule:MF_01220] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP.,Chu CH, Liu MH, Chen PC, Lin MH, Li YC, Hsiao CD, Sun YJ Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):773-83. Epub 2012 Jun 15. PMID:22751662<ref>PMID:22751662</ref> | Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP.,Chu CH, Liu MH, Chen PC, Lin MH, Li YC, Hsiao CD, Sun YJ Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):773-83. Epub 2012 Jun 15. PMID:22751662<ref>PMID:22751662</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4a7x" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Helicobacter pylori]] | [[Category: Helicobacter pylori 26695]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Chen | [[Category: Chen PC]] | ||
[[Category: Chu | [[Category: Chu CH]] | ||
[[Category: Liu | [[Category: Liu MH]] | ||
[[Category: Sun | [[Category: Sun YJ]] | ||
Latest revision as of 14:21, 20 December 2023
Crystal structure of uridylate kinase from Helicobacter pyloriCrystal structure of uridylate kinase from Helicobacter pylori
Structural highlights
FunctionPYRH_HELPY Catalyzes the reversible phosphorylation of UMP to UDP.[HAMAP-Rule:MF_01220] Publication Abstract from PubMedUridylate kinase (UMPK; EC 2.7.4.22) transfers the gamma-phosphate of ATP to UMP, forming UDP. It is allosterically regulated by GTP. Structures of Helicobacter pylori UMPK (HpUMPK) complexed with GTP (HpUMPK-GTP) and with UDP (HpUMPK-UDP) were determined at 1.8 and 2.5 A resolution, respectively. As expected, HpUMPK-GTP forms a hexamer with six GTP molecules at its centre. Interactions between HpUMPK and GTP are made by the beta3 strand of the sheet, loop beta3alpha4 and the alpha4 helix. In HpUMPK-UDP, the hexameric symmetry typical of UMPKs is absent. Only four of the HpUMPK molecules bind UDP; the other two HpUMPK molecules are in the UDP-free state. The asymmetric hexamer of HpUMPK-UDP, which has an exposed dimer interface, may assist in UDP release. Furthermore, the flexibility of the alpha2 helix, which interacts with UDP, is found to increase when UDP is absent in HpUMPK-UDP. In HpUMPK-GTP, the alpha2 helix is too flexible to be observed. This suggests that GTP binding may affect the conformation of the alpha2 helix, thereby promoting UDP release. Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP.,Chu CH, Liu MH, Chen PC, Lin MH, Li YC, Hsiao CD, Sun YJ Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):773-83. Epub 2012 Jun 15. PMID:22751662[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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