6UE0

Crystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens.

Impey, R.E.Lee, M.Hawkins, D.A.Sutton, J.M.Panjikar, S.Perugini, M.A.Soares da Costa, T.P.

(2020) FEBS Lett 594: 1453-1463

  • DOI: https://doi.org/10.1002/1873-3468.13733
  • Primary Citation of Related Structures:  
    6UE0

  • PubMed Abstract: 

    The rise of antibiotic resistance combined with the lack of new products entering the market has led to bacterial infections becoming one of the biggest threats to global health. Therefore, there is an urgent need to identify novel antibiotic targets, such as dihydrodipicolinate synthase (DHDPS), an enzyme involved in the production of essential metabolites in cell wall and protein synthesis. Here, we utilised a 7-residue sequence motif to identify mis-annotation of multiple DHDPS genes in the high-priority Gram-negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. We subsequently confirmed these mis-annotations using a combination of enzyme kinetics and X-ray crystallography. Thus, this study highlights the need to ensure genes encoding promising drug targets, like DHDPS, are annotated correctly, especially for clinically important pathogens. PDB ID: 6UE0.


  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthaseA [auth AAA],
B [auth BBB]
326Klebsiella pneumoniaeMutation(s): 0 
Gene Names: dapA_2dapA_3dapA_4dapA_5dapA_6dapA_7
EC: 4.3.3.7
UniProt
Find proteins for W9BBZ5 (Klebsiella pneumoniae)
Explore W9BBZ5 
Go to UniProtKB:  W9BBZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW9BBZ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KPI
Query on KPI
A [auth AAA],
B [auth BBB]
L-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.634α = 90
b = 114.23β = 90
c = 55.298γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE190100806
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1091976
Australian Research Council (ARC)AustraliaDP150103313

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-29
    Changes: Data collection