4-Chlorobenzoyl-CoA Ligase/Synthetase, Mutant D402P, bound to 4CB

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history


The mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase

Wu, R.Reger, A.S.Lu, X.Gulick, A.M.Dunaway-Mariano, D.

(2009) Biochemistry 48: 4115-4125

  • DOI: https://doi.org/10.1021/bi9002327
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    4-Chlorobenzoate:CoA ligase (CBL) belongs to the adenylate-forming family of enzymes that catalyze a two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site is located at the interface of a large N-terminal domain and a smaller C-terminal domain. Crystallographic structures have been determined at multiple steps along the reaction pathway and form the basis for a proposal that the C-terminal domain rotates by approximately 140 degrees between the two states that catalyze the adenylation and thioester-forming half-reactions. The domain rotation is accompanied by a change in the main chain torsional angles of Asp402, a conserved residue located at the interdomain hinge position. We have mutated the Asp402 residue to Pro in order to test the impact of reduced main chain flexibility at the putative hinge position. The crystal structure of the D402P mutant shows that the enzyme adopts the proposed adenylate-forming conformation with very little change to the overall structure. To examine the impact of this mutation on the ability of the enzyme to catalyze the complete reaction, single turnover kinetic experiments were performed. Whereas the ability of this mutant to catalyze the adenylate-forming half-reaction is reduced by approximately 3-fold, catalysis of the second half-reaction is reduced by 4 orders of magnitude. The impact of the alanine replacement of Asp402 on the thioester-forming reaction is significant, although not as dramatic as the proline mutation, and provides evidence that the Asp402 carboxylate group, through ion pair formation with N-terminal domain residue Arg400, assists in the transition to the thioester-forming conformer. Together these results support the domain alternation hypothesis.

  • Organizational Affiliation

    Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-Chlorobenzoate CoA Ligase/SynthetaseA [auth X]504Alcaligenes sp.Mutation(s): 0 
Find proteins for Q8GN86 (Alcaligenes sp. AL3007)
Explore Q8GN86 
Go to UniProtKB:  Q8GN86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GN86
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 174

Download Ideal Coordinates CCD File 
C7 H5 Cl O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.922α = 90
b = 127.922β = 90
c = 71.23γ = 120
Software Package:
Software NamePurpose
CHESSdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description