4C5B

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ATP and D-ala-D-ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.

Batson, S.de Chiara, C.Majce, V.Lloyd, A.J.Gobec, S.Rea, D.Fulop, V.Thoroughgood, C.W.Simmons, K.J.Dowson, C.G.Fishwick, C.W.G.de Carvalho, L.P.S.Roper, D.I.

(2017) Nat Commun 8: 1939-1939

  • DOI: https://doi.org/10.1038/s41467-017-02118-7
  • Primary Citation of Related Structures:  
    4C5A, 4C5B, 4C5C

  • PubMed Abstract: 

    D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure.


  • Organizational Affiliation

    School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-ALANINE--D-ALANINE LIGASE
A, B
330Escherichia coli K-12Mutation(s): 0 
EC: 6.3.2.4
UniProt
Find proteins for P07862 (Escherichia coli (strain K12))
Explore P07862 
Go to UniProtKB:  P07862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07862
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DAL
Query on DAL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
M [auth B],
N [auth B]
D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
K [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CO3
Query on CO3

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
P [auth B]
Q [auth B]
R [auth B]
G [auth A],
H [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53α = 90
b = 97.62β = 90
c = 109.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description