Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.58 kDa 
• Atom Count: 4594 
• Modelled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

1S5W

Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue Tyr133 to Phe133

• PDB DOI: 10.2210/pdb1S5W/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-01-21 Released: 2004-04-27 
• Deposition Author(s): Dobson, R.C.J., Valegard, K., Gerrard, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

The Crystal Structure of Three Site-directed Mutants of Escherichia coli Dihydrodipicolinate Synthase: Further Evidence for a Catalytic Triad

Dobson, R.C.J., Valegard, K., Gerrard, J.A.

(2004) J Mol Biol 338: 329-339

• PubMed: 15066435 
• DOI: 10.1016/j.jmb.2004.02.060
• Primary Citation of Related Structures:  
  1S5T, 1S5V, 1S5W


• PubMed Abstract: 
  

Dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52) catalyses the branchpoint reaction of lysine biosynthesis in plants and microbes: the condensation of (S)-aspartate-beta-semialdehyde and pyruvate. The crystal structure of wild-type DHDPS has been published to 2.5A, revealing a tetrameric molecule comprised of four identical (beta/alpha)(8)-barrels, each containing one active site. Previous workers have hypothesised that the catalytic mechanism of the enzyme involves a catalytic triad of amino acid residues, Tyr133, Thr44 and Tyr107, which provide a proton shuttle to transport protons from the active site to solvent. We have tested this hypothesis using site-directed mutagenesis to produce three mutant enzymes: DHDPS-Y133F, DHDPS-T44V and DHDPS-Y107F. Each of these mutants has substantially reduced activity, consistent with the catalytic triad hypothesis. We have determined each mutant crystal structure to at least 2.35A resolution and compared the structures to the wild-type enzyme. All mutant enzymes crystallised in the same space group as the wild-type form and only minor differences in structure are observed. These results suggest that the catalytic triad is indeed in operation in wild-type DHDPS.

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Organizational Affiliation: 

Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	292	Escherichia coli	Mutation(s): 1  Gene Names: dapA EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2  Go to UniProtKB:  P0A6L2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.206	α = 90
b = 121.206	β = 90
c = 110.784	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-21 
• Released Date: 2004-04-27 
Deposition Author(s): Dobson, R.C.J., Valegard, K., Gerrard, J.A.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references