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

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

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

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

(2018) Biochemistry 57: 963-977

  • DOI: https://doi.org/10.1021/acs.biochem.7b01137
  • Primary Citation of Related Structures:  
    4WEQ, 4Z0P, 5J23, 5UNN, 5UOG, 5V6Q, 5V72, 5V7G, 5V7N

  • 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.

  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia , 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADPH-dependent glyoxylate/hydroxypyruvate reductase
A, B, C, D
323Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: SMc04462
Find proteins for Q92LZ4 (Rhizobium meliloti (strain 1021))
Explore Q92LZ4 
Go to UniProtKB:  Q92LZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92LZ4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
C21 H28 N7 O17 P3
Query on MLA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
N [auth D]
C3 H4 O4
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: H 3
  • Diffraction Data: https://doi.org/10.18430/M35V6Q
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.484α = 90
b = 176.484β = 90
c = 135.857γ = 120
Software Package:
Software NamePurpose
MD2data collection
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117080
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesHG008424

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Refinement description
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description