Abstract
Burkholderia phymatum is an important symbiotic nitrogen-fixing betaproteobacterium. B. phymatum is beneficial, unlike other Burkholderia species, which cause disease or are potential bioagents. Structural genomics studies at the SSGCID include characterization of the structures of short-chain dehydrogenases/reductases (SDRs) from multiple Burkholderia species. The crystal structure of a short-chain dehydrogenase from B. phymatum (BpSDR) was determined in space group C2221 at a resolution of 1.80 Å. BpSDR shares less than 38% sequence identity with any known structure. The monomer is a prototypical SDR with a well conserved cofactor-binding domain despite its low sequence identity. The substrate-binding cavity is unique and offers insights into possible functions and likely inhibitors of the enzymatic functions of BpSDR.
Highlights
Burkholderia are nonfermenting motile Gram-negative bacteria that are among the largest groups of species of Betaproteobacteria and include infective and symbiotic species (Yabuuchi et al, 1992; Sawana et al, 2014)
Recombinant BpSDR was purified by the standard two-step protocol consisting of immobilized metal-affinity chromatography (IMAC) followed by size-exclusion chromatography (SEC) at SSGCID
The molecular replacement (MR) search model was the structure of a Rv0851c ortholog short-chain dehydrogenase from Mycobacterium paratuberculosis (PDB entry 3tjr; Baugh et al, 2015), the structure with the closest amino-acid sequence identity to BpSDR (38% at over 89% coverage)
Summary
Burkholderia are nonfermenting motile Gram-negative bacteria that are among the largest groups of species of Betaproteobacteria and include infective and symbiotic species (Yabuuchi et al, 1992; Sawana et al, 2014). Due to the importance of Burkholderia, there is a need to clarify the structures of enzymes that play important roles in the life cycles of these bacteria. The SSGCID has characterized the structures of proteins that may play important roles in these bacteria. The protein structure reported here is a putative SDR which shares less than 38% sequence identity with any published structure. This structure is part of structural genomics efforts at the Seattle Structural Genomics Center for Infectious Disease (Raymond et al, 2011; Myler et al, 2009; Baugh et al, 2013). Vapor diffusion, sitting drop 287 45 300 mM NaCl, 20 mM HEPES, 5% glycerol, 1 mM TCEP pH 7.0 MCSG1 C4: 170 mM ammonium acetate, 85 mM sodium acetate–HCl pH 4.6, 25.5%(w/v) PEG 4000, 15%(v/v) glycerol, 4 mM NAD 0.4 ml:0.4 ml
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