1VPD

X-Ray Crystal Structure of Tartronate Semialdehyde Reductase [Salmonella Typhimurium LT2]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium.

Osipiuk, J., Zhou, M., Moy, S., Collart, F., Joachimiak, A.

(2009) J Struct Funct Genomics 10: 249-253

  • DOI: https://doi.org/10.1007/s10969-009-9059-x
  • Primary Citation of Related Structures:  
    1VPD, 1YB4

  • PubMed Abstract: 

    Tartronate semialdehyde reductases (TSRs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using NAD as cofactor in the final stage of D-glycerate biosynthesis. These enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. Here, we present the crystal structure of GarR a TSR from Salmonella typhimurium determined by the single-wavelength anomalous diffraction method and refined to 1.65 A resolution. The active site of the enzyme contains L-tartrate which most likely mimics a position of a glycerate which is a product of the enzyme reaction. The analysis of the TSR structure shows also a putative NADPH binding site in the enzyme.

    • Organizational Affiliation: 

    Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Bldg 202, Argonne, IL 60439, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TARTRONATE SEMIALDEHYDE REDUCTASE299Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: GARR
UniProt
Find proteins for Q8ZLV8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZLV8 
Go to UniProtKB:  Q8ZLV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZLV8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.275α = 90
b = 105.428β = 90
c = 155.045γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations