1VPD

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

• PDB DOI: https://doi.org/10.2210/pdb1VPD/pdb
• Entry: 1VPD supersedes: 1TEA

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-22 Released: 2004-10-26 
• Deposition Author(s): Osipiuk, J., Zhou, M., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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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 

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

• PubMed: 19184529 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.92 kDa 
• Atom Count: 2,734 
• Modelled Residue Count: 294 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TARTRONATE SEMIALDEHYDE REDUCTASE	A	299	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: GARR EC: 1.1.1.60
UniProt
Find proteins for Q8ZLV8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZLV8  Go to UniProtKB:  Q8ZLV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 55.275	α = 90
b = 105.428	β = 90
c = 155.045	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Osipiuk, J., Zhou, M., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 1TEA

Revision History  

• 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
• Version 1.4: 2024-10-30
  Changes: Structure summary