PDBsum entry 4z0p

Oxidoreductase

PDB id: 4z0p

Contents

Protein chain

316 a.a.

Ligands

OXD ×2

EPE

GOL ×2

NDP

Metals

_CL

Waters ×429

PDB id:

4z0p

Name:

Oxidoreductase

Title:

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase smc02828 (smghra) from sinorhizobium meliloti in complex with NADPH and oxalate

Structure:

NAD-dependent dehydrogenase. Chain: a. Engineered: yes

Source:

Rhizobium meliloti (strain 1021). Ensifer meliloti. Organism_taxid: 266834. Strain: 1021. Gene: r00152, smc02828. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.135 R-free: 0.150

Authors:

P.Sroka,O.A.Gasiorowska,K.B.Handing,I.G.Shabalin,P.J.Porebski, B.S.Hillerich,J.Bonanno,S.C.Almo,W.Minor,New York Structural Genomics Research Consortium (Nysgrc)

Key ref:

J.Kutner et al. (2018). Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry, 57, 963-977. PubMed id: 29309127 DOI: 10.1021/acs.biochem.7b01137

Date:

26-Mar-15 Release date: 08-Apr-15

Protein chain

Q92T34  (Q92T34_RHIME) -  NAD-dependent dehydrogenase from Rhizobium meliloti (strain 1021)

Seq: 319 a.a.

Struc: 316 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.79 - glyoxylate reductase (NADP(+)).
• Reaction: glycolate + NADP⁺ = glyoxylate + NADPH + H⁺

glycolate (Bound ligand (Het Group name = OXD) matches with 83.33% similarity) + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = glyoxylate + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acs.biochem.7b01137

Biochemistry 57:963-977 (2018)

PubMed id: 29309127

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.

J.Kutner, I.G.Shabalin, D.Matelska, K.B.Handing, O.Gasiorowska, P.Sroka, M.W.Gorna, K.Ginalski, K.Wozniak, W.Minor.

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.