3qdk | pdb_00003qdk

Structural insight on mechanism and diverse substrate selection strategy of ribulokinase

spinqualitylabelsall models 3qdk, resolution 2.31Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3qdk is a 4 chain structure with sequence from Bacillus halodurans. This structure supersedes the now removed PDB entry 3jvp. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: QDK Gene: araB, BH1872 (Bacillus halodurans) Activity: Ribulokinase, with EC number 2.7.1.16 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed 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. Proteins 2012; (c) 2011 Wiley Periodicals, Inc. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.,Agarwal R, Burley SK, Swaminathan S Proteins. 2012 Jan;80(1):261-8. doi: 10.1002/prot.23202. Epub 2011 Nov 9. PMID:22072612 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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