1YB4

Crystal Structure of the Tartronic Semialdehyde Reductase from Salmonella typhimurium LT2

• PDB DOI: https://doi.org/10.2210/pdb1YB4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-12-20 Released: 2005-02-01 
• Deposition Author(s): Kim, Y., Wu, R., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.304 
• R-Value Work: 0.229 
• R-Value Observed: 0.236 

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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.59 kDa 
• Atom Count: 4,533 
• Modelled Residue Count: 582 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tartronic semialdehyde reductase	A, B	295	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 11  EC: 1.1.1.60
UniProt
Find proteins for Q8ZR83 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZR83  Go to UniProtKB:  Q8ZR83

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.304 
• R-Value Work: 0.229 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.335	α = 90
b = 134.255	β = 90
c = 48.216	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Kim, Y., Wu, R., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary