4GDM

Crystal Structure of E.coli MenH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of E. coli Native MenH and Two Active Site Mutants.

Johnston, J.M.Jiang, M.Guo, Z.Baker, E.N.

(2013) Plos One 8: e61325-e61325

  • DOI: 10.1371/journal.pone.0061325
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent revision of the biosynthetic pathway for menaquinone has led to the discovery of a previously unrecognized enzyme 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, also known as MenH. This enzyme has an α/β hydrolase fold with a ...

    Recent revision of the biosynthetic pathway for menaquinone has led to the discovery of a previously unrecognized enzyme 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, also known as MenH. This enzyme has an α/β hydrolase fold with a catalytic triad comprising Ser86, His232, and Asp210. Mutational studies identified a number of conserved residues of importance to activity, and modeling further implicated the side chains of Tyr85 and Trp147 in formation of a non-standard oxyanion hole. We have solved the structure of E. coli MenH (EcMenH) at 2.75 Å resolution, together with the structures of the active site mutant proteins Tyr85Phe and Arg124Ala, both at 2.5 Å resolution. EcMenH has the predicted α/β hydrolase fold with its core α/β domain capped by a helical lid. The active site, a long groove beneath the cap, contains a number of conserved basic residues and is found to bind exogeneous anions, modeled as sulfate and chloride, in all three crystal structures. Docking studies with the MenH substrate and a transition state model indicate that the bound anions mark the binding sites for anionic groups on the substrate. The docking studies, and careful consideration of the active site geometry, further suggest that the oxyanion hole is of a conventional nature, involving peptide NH groups, rather than the proposed site involving Tyr85 and Trp147. This is in accord with conclusions from the structure of S. aureus MenH. Comparisons with the latter do, however, indicate differences in the periphery of the active site that could be of relevance to selective inhibition of MenH enzymes.


    Organizational Affiliation

    Maurice Wilkins Centre and School of Biological Sciences, University of Auckland, Auckland, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
A, B, C
268Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: menH (yfbB)
EC: 4.2.99.20
Find proteins for P37355 (Escherichia coli (strain K12))
Go to UniProtKB:  P37355
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.664α = 90.00
b = 116.664β = 90.00
c = 476.949γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
BUSTER-TNTrefinement
BUSTERrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data scaling
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Structure summary
  • Version 1.3: 2017-11-15
    Type: Refinement description