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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

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