2EUA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/bi0608515

  • 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 stru ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Menaquinone-specific isochorismate synthase
A, B
431Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: menF (yfbA)
EC: 5.4.4.2
Find proteins for P38051 (Escherichia coli (strain K12))
Go to UniProtKB:  P38051
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download SDF File 
Download CCD File 
A, B
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 146.408α = 90.00
b = 146.408β = 90.00
c = 125.600γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description