3QDK

Structural insight on mechanism and diverse substrate selection strategy of ribulokinase

「3JVP」から置き換えられました

3QDK の概要

• エントリーDOI: 10.2210/pdb3qdk/pdb
• 分子名称: Ribulokinase, L-ribulose (3 entities in total)
• 機能のキーワード: structural genomics, psi-2, protein structure initiative, new york sgx research center for structural genomics, nysgxrc, psi-ii, arabinose catabolism, atp binding, transferase
• 由来する生物種: Bacillus halodurans
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 251567.25

構造登録者

Agarwal, R.,Burley, S.K.,Swaminathan, S.,New York SGX Research Center for Structural Genomics (NYSGXRC) (登録日: 2011-01-18, 公開日: 2011-02-09, 最終更新日: 2024-02-21)

主引用文献

Agarwal, R.,Burley, S.K.,Swaminathan, S.
Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.
Proteins, 80:261-268, 2012

PubMed Abstract: The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k(cat) values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified (447)GGLPQK(452) as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.

PubMed: 22072612
DOI: 10.1002/prot.23202

実験手法

X-RAY DIFFRACTION (2.31 Å)