3BZM

Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF

• PDB DOI: https://doi.org/10.2210/pdb3BZM/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-18 Released: 2008-05-20 
• Deposition Author(s): Parsons, J.F., Shi, K.M., Ladner, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.308 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 

Literature

Structure of isochorismate synthase in complex with magnesium.

Parsons, J.F., Shi, K.M., Ladner, J.E.

(2008) Acta Crystallogr D Biol Crystallogr 64: 607-610

• PubMed: 18453696 
• DOI: https://doi.org/10.1107/S0907444908005477
• Primary Citation of Related Structures:  
  3BZM, 3BZN


• PubMed Abstract: 
  

  The electron carrier menaquinone is one of many important bacterial metabolites that are derived from the key intermediate chorismic acid. MenF, the first enzyme in the menaquinone pathway, catalyzes the isomerization of chorismate to isochorismate. Here, an improved structure of MenF in a new crystal form is presented. The structure, solved at 2.0 angstroms resolution in complex with magnesium, reveals a well defined closed active site. Existing evidence suggests that the mechanism of the reaction catalyzed by MenF involves nucleophilic attack of a water molecule on the chorismate ring. The structure reveals a well defined water molecule located in an appropriate position for activation by Lys190 and attack on the substrate.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.02 kDa 
• Atom Count: 3,546 
• Modelled Residue Count: 429 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinone-specific isochorismate synthase	A	431	Escherichia coli	Mutation(s): 0  Gene Names: menF, yfbA EC: 5.4.4.2
UniProt
Find proteins for P38051 (Escherichia coli (strain K12)) Explore P38051  Go to UniProtKB:  P38051

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.308 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.37	α = 90
b = 72.37	β = 90
c = 164.01	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Parsons, J.F., Shi, K.M., Ladner, J.E.

Revision History  

• Version 1.0: 2008-05-20
  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