5J23

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

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: 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 ...

    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 Chemistry, University of Warsaw , 1 Ludwika Pasteura, 02-093 Warsaw, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-hydroxyacid dehydrogenaseA, B, C, D323Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: SMc04462
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2R
Query on A2R

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
R [auth D]
[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
C15 H24 N5 O17 P3
ICNHOLCERMYLRZ-KEOHHSTQSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: H 3
  • Diffraction Data DOI: 10.18430/M35J23 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.822α = 90
b = 175.822β = 90
c = 136.839γ = 120
Software Package:
Software NamePurpose
MD2data collection
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references, Derived calculations
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.4: 2018-05-23
    Changes: Data collection, Experimental preparation, Structure summary
  • Version 1.5: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.6: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.7: 2022-04-13
    Changes: Database references, Structure summary