1QXO

Crystal structure of Chorismate synthase complexed with oxidized FMN and EPSP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction

Maclean, J.Ali, S.

(2003) Structure 11: 1499-1511

  • DOI: 10.1016/j.str.2003.11.005
  • Primary Citation of Related Structures:  
    1QXO

  • PubMed Abstract: 
  • The crystal structure of chorismate synthase (CS) from Streptococcus pneumoniae has been solved to 2.0 A resolution in the presence of flavin mononucleotide (FMN) and the substrate 5-enolpyruvyl-3-shikimate phosphate (EPSP). CS catalyses the final step of the shikimate pathway and is a potential therapeutic target for the rational design of novel antibacterials, antifungals, antiprotozoals, and herbicides ...

    The crystal structure of chorismate synthase (CS) from Streptococcus pneumoniae has been solved to 2.0 A resolution in the presence of flavin mononucleotide (FMN) and the substrate 5-enolpyruvyl-3-shikimate phosphate (EPSP). CS catalyses the final step of the shikimate pathway and is a potential therapeutic target for the rational design of novel antibacterials, antifungals, antiprotozoals, and herbicides. CS is a tetramer with the monomer possessing a novel beta-alpha-beta fold. The interactions between the enzyme, cofactor, and substrate reveal the structural reasons underlying the unique catalytic mechanism and identify the amino acids involved. This structure provides the essential initial information necessary for the generation of novel anti-infective compounds by a structure-guided medicinal chemistry approach.


    Organizational Affiliation

    Department of Structural Biology, West of Scotland Science Park, Glasgow G20 0XP, Scotland, United Kingdom. john.maclean@btinternet.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chorismate synthaseA, B, C, D388Streptococcus pneumoniaeMutation(s): 12 
Gene Names: aroCSP1374 OR SPR1232
EC: 4.2.3.5
Find proteins for P0A2Y6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P0A2Y6 
Go to UniProtKB:  P0A2Y6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
BA [auth D], CA [auth D], K [auth A], P [auth B], U [auth C], V [auth C]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
EPS
Query on EPS

Download Ideal Coordinates CCD File 
DA [auth D], L [auth A], Q [auth B], W [auth C]5-[(1-CARBOXYVINYL)OXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C10 H13 O10 P
QUTYKIXIUDQOLK-PRJMDXOYSA-N
 Ligand Interaction
NCO
Query on NCO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , M [auth B] , N [auth B] , R [auth C] , S [auth C] , X [auth D] , 
E [auth A],  F [auth A],  G [auth A],  M [auth B],  N [auth B],  R [auth C],  S [auth C],  X [auth D],  Y [auth D]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D], H [auth A], I [auth A], J [auth A], O [auth B], T [auth C], Z [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd:  20   nM  Binding MOAD
FMNKd:  20000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.059α = 90
b = 124.582β = 115.15
c = 85.163γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2003-09-08 
  • Released Date: 2003-12-23 
  • Deposition Author(s): Maclean, J., Ali, S.

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description