9S3L | pdb_00009s3l

ClxA from Clostridium cavendishii (apo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.301 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biocatalytic synthesis of phenyl benzoate esters using the amide ligase ClxA.

Ascham, A.Tang, Q.Fairlamb, I.J.S.Grogan, G.

(2025) RSC Chem Biol 6: 1879-1884

  • DOI: https://doi.org/10.1039/d5cb00205b
  • Primary Citation of Related Structures:  
    9S3L

  • PubMed Abstract: 

    The synthesis of ester bonds using lipases is one of the most frequently performed reactions in biocatalysis, yet examples of the enzymatic synthesis of phenyl benzoate esters are comparatively rare. In this report we show that the ligase ClxA, from Clostridium cavendishii , initially reported to have roles in amide bond formation in the biosynthesis of benzoxazole antibiotics, is an effective catalyst for the formation of phenyl benzoate esters from acid and phenol substrates using ATP in an aqueous medium. The structure of ClxA in a complex with both AMP and 3,4-aminohydroxybenzoic acid was determined by X-ray crystallography to 2.15 Å resolution and used as a platform to engineer the enzyme to create variants N226L and K140A possessing broader substrate specificity for ester formation, and also the ability to enable the synthesis of native amide product oligomers.


  • Organizational Affiliation
    • Department of Chemistry, University of York Heslington York YO10 5DD UK gideon.grogan@york.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylacetate-CoA ligase
A, B, C, D
401Clostridium cavendishiiMutation(s): 0 
Gene Names: SAMN02745163_01864
UniProt
Find proteins for A0A1M6IZB6 (Clostridium cavendishii DSM 21758)
Explore A0A1M6IZB6 
Go to UniProtKB:  A0A1M6IZB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M6IZB6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.301 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.94α = 90.26
b = 79.97β = 95.58
c = 81.77γ = 103.5
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references