3pdu | pdb_00003pdu
Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter sulfurreducens in complex with NADP+
Structural highlights
Publication Abstract from PubMedBeta-hydroxyacid dehydrogenase (beta-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD(+)- or NADP(+)-dependent oxidation of various beta-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple beta-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential beta-HAD genes. The protein sequences of one pair of these genes, Gs-betaHAD (Q74DE4) and Gm-betaHAD (Q39R98), have 65% sequence identity and 77% sequence similarity with each other. Both proteins are observed to reduce succinic semialdehyde, a 4-carbon substrate instead of the typical beta-HAD 3-carbon substrate, to gamma-hydroxybutyric acid. To further explore the structural and functional characteristics of these two beta-HADs with a less frequently observed substrate specificity, crystal structures for Gs-betaHAD and Gm-betaHAD in complex with NADP(+) were determined to a resolution of 1.89 A and 2.07 A, respectively. The structures of both proteins are similar, composed of 14 alpha-helices and nine beta-strands organized into two domains. Domain 1 (1-165) adopts a typical Rossmann fold composed of two alpha/beta units: a six-strand parallel beta-sheet surrounded by six alpha-helices (alpha1-alpha6) followed by a mixed three-strand beta-sheet surrounded by two alpha-helices (alpha7 and alpha8). Domain 2 (166-287) is composed of a bundle of seven alpha-helices (alpha9-alpha14). Four functional regions conserved in all beta-HADs are spatially located near each other, with a buried molecule of NADP(+), at the interdomain cleft. Comparison of these Geobacter structures to a closely related beta-HAD from Arabidopsis thaliana in the apo-NADP(+) and apo-substrate bound state suggests that NADP(+) binding effects a rigid body rotation between Domains 1 and 2. Bound near the Substrate-Binding and Catalysis Regions in two of the eight protomers in the asymmetric unit of Gm-betaHAD is a glycerol molecule that may mimic features of bound biological substrates. Structural characterization of a beta-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity.,Zhang Y, Zheng Y, Qin L, Wang S, Buchko GW, Garavito RM Biochimie. 2014 Sep;104:61-9. doi: 10.1016/j.biochi.2014.05.002. Epub 2014 May, 27. PMID:24878278[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
| ||||||||||||||||||||||
