1UM0 | pdb_00001um0

Crystal structure of chorismate synthase complexed with FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.243 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of chorismate synthase: a novel FMN-binding protein fold and functional insights

Ahn, H.J.Yoon, H.J.Lee, B.Suh, S.W.

(2004) J Mol Biology 336: 903-915

  • DOI: https://doi.org/10.1016/j.jmb.2003.12.072
  • Primary Citation Related Structures: 
    1UM0, 1UMF

  • PubMed Abstract: 

    Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate to chorismate in the shikimate pathway, which represents an attractive target for discovering antimicrobial agents and herbicides. Chorismate serves as a common precursor for the synthesis of aromatic amino acids and many aromatic compounds in microorganisms and plants. Chorismate synthase requires reduced FMN as a cofactor but the catalyzed reaction involves no net redox change. Here, we have determined the crystal structure of chorismate synthase from Helicobacter pylori in both FMN-bound and FMN-free forms. It is a tetrameric enzyme, with each monomer possessing a novel "beta-alpha-beta sandwich fold". Highly conserved regions, including several flexible loops, cluster together around the bound FMN to form the active site. The unique FMN-binding site is formed largely by a single subunit, with a small contribution from a neighboring subunit. The isoalloxazine ring of the bound FMN is significantly non-planar. Our structure illuminates the essential functional roles played by the cofactor.


  • Organizational Affiliation
    • Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-0742, South Korea.

Macromolecule Content 

  • Total Structure Weight: 162.45 kDa 
  • Atom Count: 11,843 
  • Modeled Residue Count: 1,460 
  • Deposited Residue Count: 1,460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chorismate synthase
A, B, C, D
365Helicobacter pyloriMutation(s): 0 
Gene Names: AROC
EC: 4.2.3.5
UniProt
Find proteins for P56122 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56122 
Go to UniProtKB:  P56122
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56122
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.243 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.686α = 90
b = 146.686β = 90
c = 132.31γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations