4A7X

Crystal structure of uridylate kinase from Helicobacter pylori

4A7X の概要

• エントリーDOI: 10.2210/pdb4a7x/pdb
• 関連するPDBエントリー: 4A7W
• 分子名称: URIDYLATE KINASE, URIDINE-5'-DIPHOSPHATE (3 entities in total)
• 機能のキーワード: transferase
• 由来する生物種: HELICOBACTER PYLORI
• 細胞内の位置: Cytoplasm (By similarity): P56106
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 158867.34

構造登録者

Chu, C.H.,Liu, M.H.,Chen, P.C.,Sun, Y.J. (登録日: 2011-11-15, 公開日: 2012-06-27, 最終更新日: 2023-12-20)

主引用文献

Chu, 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

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

実験手法

X-RAY DIFFRACTION (2.49 Å)