dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate bound to the active site

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine.

Conly, C.J.Skovpen, Y.V.Li, S.Palmer, D.R.Sanders, D.A.

(2014) Biochemistry 53: 7396-7406

  • DOI: https://doi.org/10.1021/bi5012157
  • Primary Citation of Related Structures:  
    4LY8, 4M19, 4MLJ, 4MLR, 4R53

  • PubMed Abstract: 

    Dihydrodipicolinate synthase (DHDPS), an enzyme found in most bacteria and plants, controls a critical step in the biosynthesis of l-lysine and meso-diaminopimelate, necessary components for bacterial cell wall biosynthesis. DHDPS catalyzes the condensation of pyruvate and (S)-aspartate-β-semialdehyde, forming an unstable product that is dehydrated to dihydrodipicolinate. The tetrameric enzyme is allosterically inhibited by l-lysine, and a better understanding of the allosteric inhibition mechanism is necessary for the design of potent antibacterial therapeutics. Here we describe the high-resolution crystal structures of DHDPS from Campylobacter jejuni with and without its inhibitor bound to the allosteric sites. These structures reveal a role for Y110 in the regulation of the allosteric inhibition by lysine. Mutation of Y110 to phenylalanine results in insensitivity to lysine inhibition, although the mutant crystal structure reveals that lysine does bind in the allosteric site. Comparison of the lysine-bound Y110F structure with wild-type structures reveals that key structural changes due to lysine binding are absent in this mutant.

  • Organizational Affiliation

    Department of Chemistry, University of Saskatchewan , 110 Science Place, Saskatoon, SK S7N 5C9, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dihydrodipicolinate synthase
A, B, C, D
306Campylobacter jejuniMutation(s): 1 
Gene Names: dapA
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q9PPB4 
Go to UniProtKB:  Q9PPB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PPB4
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on KPI
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.61α = 90
b = 97.24β = 90
c = 148.46γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MxDCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Data collection
  • Version 1.2: 2015-04-01
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-29
    Changes: Data collection