5V72

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with citrate

Summary for 5V72

• Entry DOI: 10.2210/pdb5v72/pdb
• Related: 5J23 5UOG 5V6Q
• Descriptor: NADPH-dependent glyoxylate/hydroxypyruvate reductase, SODIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: nadph-dependent glyoxylate/hydroxypyruvate reductase, nadp, nysgrc, sinorhizobium meliloti, structural genomics, psi-biology, new york structural genomics research consortium, oxidoreductase
• Biological source: Rhizobium meliloti (strain 1021) (Ensifer meliloti)
• Total number of polymer chains: 4
• Total formula weight: 137626.65

Authors

Shabalin, I.G.,Handing, K.B.,Gasiorowska, O.A.,Cooper, D.R.,Matelska, D.,Bonanno, J.,Almo, S.C.,Minor, W.,New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2017-03-17, release date: 2017-03-29, Last modification date: 2023-10-04)

Primary citation

Kutner, J.,Shabalin, I.G.,Matelska, D.,Handing, K.B.,Gasiorowska, O.,Sroka, P.,Gorna, M.W.,Ginalski, K.,Wozniak, K.,Minor, W.
Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Biochemistry, 57:963-977, 2018

PubMed Abstract: The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.

PubMed: 29309127
DOI: 10.1021/acs.biochem.7b01137

Experimental method

X-RAY DIFFRACTION (2.1 Å)