2EUA | pdb_00002eua

Structure and Mechanism of MenF, the Menaquinone-Specific Isochorismate Synthase from Escherichia Coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.276 (Depositor) 
  • R-Value Work: 
    0.229 (Depositor) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2EUA

This is version 1.4 of the entry. See complete history

Literature

Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family.

Kolappan, S.Zwahlen, J.Zhou, R.Truglio, J.J.Tonge, P.J.Kisker, C.

(2007) Biochemistry 46: 946-953

  • DOI: https://doi.org/10.1021/bi0608515
  • Primary Citation Related Structures: 
    2EUA

  • PubMed Abstract: 

    Menaquinone biosynthesis is initiated by the conversion of chorismate to isochorismate, a reaction that is catalyzed by the menaquinone-specific isochorismate synthase, MenF. The catalytic mechanism of MenF has been probed using a combination of structural and biochemical studies, including the 2.5 A structure of the enzyme, and Lys190 has been identified as the base that activates water for nucleophilic attack at the chorismate C2 carbon. MenF is a member of a larger family of Mg2+ dependent chorismate binding enzymes catalyzing distinct chorismate transformations. The studies reported here extend the mechanism recently proposed for this enzyme family by He et al.: He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-85.


  • Organizational Affiliation
    • Department of Pharmacological Sciences and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5115, USA.

Macromolecule Content 

  • Total Structure Weight: 97.95 kDa 
  • Atom Count: 6,863 
  • Modeled Residue Count: 856 
  • Deposited Residue Count: 862 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Menaquinone-specific isochorismate synthase
A, B
431Escherichia coliMutation(s): 0 
Gene Names: menF
EC: 5.4.4.2
UniProt
Find proteins for P38051 (Escherichia coli (strain K12))
Explore P38051 
Go to UniProtKB:  P38051
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38051
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.276 (Depositor) 
  • R-Value Work:  0.229 (Depositor) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.408α = 90
b = 146.408β = 90
c = 125.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description