2I80

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.

Liu, S.Chang, J.S.Herberg, J.T.Horng, M.M.Tomich, P.K.Lin, A.H.Marotti, K.R.

(2006) Proc.Natl.Acad.Sci.Usa 103: 15178-15183

  • DOI: 10.1073/pnas.0604905103
  • Primary Citation of Related Structures:  2I87, 2I8C

  • PubMed Abstract: 
  • D-alanine:D-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. It catalyzes the formation of D-alanine:D-alanine dipeptide, sequentially by using one D-alanine and o ...

    D-alanine:D-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. It catalyzes the formation of D-alanine:D-alanine dipeptide, sequentially by using one D-alanine and one ATP as substrates for the first-half reaction, and a second D-alanine substrate to complete the reaction. Some gain of function DDl mutants can use an alternate second substrate, causing resistance to vancomycin, one of the last lines of defense against life-threatening Gram-positive infections. Here, we report the crystal structure of Staphylococcus aureus DDl (StaDDl) and its cocrystal structures with 3-chloro-2,2-dimethyl-N-[4(trifluoromethyl)phenyl]propanamide (inhibitor 1) (Ki=4 microM against StaDDl) and with ADP, one of the reaction products, at resolutions of 2.0, 2.2, and 2.6 A, respectively. The overall structure of StaDDl can be divided into three distinct domains. The inhibitor binds to a hydrophobic pocket at the interface of the first and the third domain. This inhibitor-binding pocket is adjacent to the first D-alanine substrate site but does not overlap with any substrate sites. An allosteric inhibition mechanism of StaDDl by this compound was proposed. The mechanism provides the basis for developing new antibiotics targeting D-alanine:D-alanine ligase. Because this compound only interacts with residues from the first D-alanine site, inhibitors with this binding mode potentially could overcome vancomycin resistance.


    Organizational Affiliation

    Pfizer, Inc., Eastern Point Road, Groton, CT 06340, USA. shenping.liu@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanine-D-alanine ligase
A, B
360Staphylococcus aureus (strain COL)Gene Names: ddl
EC: 6.3.2.4
Find proteins for Q5HEB7 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HEB7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G1L
Query on G1L

Download SDF File 
Download CCD File 
A, B
3-CHLORO-2,2-DIMETHYL-N-[4-(TRIFLUOROMETHYL)PHENYL]PROPANAMIDE
C12 H13 Cl F3 N O
QCQZFHOGRCQNIH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G1LKi: 4000 nM BINDINGMOAD
G1LKi: 4000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.730α = 90.00
b = 66.082β = 96.57
c = 78.789γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance