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4A7W

Crystal structure of uridylate kinase from Helicobacter pylori

Summary for 4A7W
Entry DOI10.2210/pdb4a7w/pdb
Related4A7X
DescriptorURIDYLATE KINASE, GUANOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... (4 entities in total)
Functional Keywordstransferase
Biological sourceHELICOBACTER PYLORI
Cellular locationCytoplasm (By similarity): P56106
Total number of polymer chains2
Total formula weight53647.45
Authors
Chu, C.H.,Chen, P.C.,Liu, M.H.,Sun, Y.J. (deposition date: 2011-11-15, release date: 2012-06-27, Last modification date: 2023-12-20)
Primary citationChu, C.H.,Chen, P.C.,Liu, M.H.,Li, Y.C.,Hsiao, C.D.,Sun, Y.J.
Structures of Helicobacter Pylori Uridylate Kinase: Insight Into Release of the Product Udp
Acta Crystallogr.,Sect.D, 68:773-, 2012
Cited by
PubMed Abstract: Uridylate kinase (UMPK; EC 2.7.4.22) transfers the γ-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 Å 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 β3 strand of the sheet, loop β3α4 and the α4 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 α2 helix, which interacts with UDP, is found to increase when UDP is absent in HpUMPK-UDP. In HpUMPK-GTP, the α2 helix is too flexible to be observed. This suggests that GTP binding may affect the conformation of the α2 helix, thereby promoting UDP release.
PubMed: 22751662
DOI: 10.1107/S0907444912011407
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.8 Å)
Structure validation

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