Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, Solved at 1.98 Angstroms

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.3 of the entry. See complete history


Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase

Chen, Y.Sun, Y.Song, H.Guo, Z.

(2015) J Biol Chem 290: 23971-23983

  • DOI: https://doi.org/10.1074/jbc.M115.676304
  • Primary Citation of Related Structures:  
    5BUQ, 5BUR, 5BUS

  • PubMed Abstract: 

    o-Succinylbenzoyl-CoA synthetase, or MenE, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. Using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between ATP and adenylating enzymes, including acyl/aryl-CoA synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. It involves tight gripping interactions of the phosphate-binding loop (P-loop) with the ATP triphosphate moiety and an open-closed conformational change to form a compact adenylation active site. In MenE catalysis, this ATP-enzyme interaction creates a new binding site for the carboxylate substrate, allowing revelation of the determinants of substrate specificities and in-line alignment of the two substrates for backside nucleophilic substitution reaction by molecular modeling. In addition, the ATP-enzyme interaction is suggested to play a crucial catalytic role by mutation of the P-loop residues hydrogen-bonded to ATP. Moreover, the ATP-enzyme interaction has also clarified the positioning and catalytic role of a conserved lysine residue in stabilization of the transition state. These findings provide new insights into the adenylation half-reaction in the domain alteration catalytic mechanism of the adenylate-forming enzymes.

  • Organizational Affiliation

    From the Department of Chemistry and State Key Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinylbenzoate--CoA ligase
A, B
494Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: menEBSU30790
Find proteins for P23971 (Bacillus subtilis (strain 168))
Explore P23971 
Go to UniProtKB:  P23971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23971
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.78α = 90
b = 76.91β = 114.93
c = 93.87γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Cootmodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
HKSAR GovernmentHong KongGRF601413

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Data collection
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description