Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase
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{sub 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 {sup 447}{und GG}LPQ{und K}{sup 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.
- Research Organization:
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Sponsoring Organization:
- ELI LILLY & COMPANY
- DOE Contract Number:
- DE-AC02-98CH10886
- OSTI ID:
- 1044005
- Report Number(s):
- BNL-96553-2012-JA; PSFGEY; 600301010; TRN: US201214%%260
- Journal Information:
- Proteins, Vol. 80, Issue 1; ISSN 0887-3585
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
59 BASIC BIOLOGICAL SCIENCES
ARABINOSE
BACILLUS
CATABOLISM
CHAINS
CLOSURES
CRYSTAL STRUCTURE
ENZYMES
HYDROGEN
MONOSACCHARIDES
NITROGEN
PHOSPHORYLATION
PHOSPHOTRANSFERASES
POLYPEPTIDES
RIBULOSE
SACCHARIDES
SACCHAROSE
SUBSTRATES
crystal structure
ribulokinase
ribulose
araBAD
araB
arabinose
catabolism