PDBsum entry 1umf

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Lyase PDB id
Protein chains
365 a.a. *
Waters ×492
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of chorismate synthase
Structure: Chorismate synthase. Chain: a, b, c, d. Synonym: 5-enolpyruvylshikimate-3-phosphate phospholyase. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 210. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
2.25Å     R-factor:   0.202     R-free:   0.248
Authors: H.J.Ahn,H.J.Yoon,B.Lee,S.W.Suh
Key ref:
H.J.Ahn et al. (2004). Crystal structure of chorismate synthase: a novel FMN-binding protein fold and functional insights. J Mol Biol, 336, 903-915. PubMed id: 15095868 DOI: 10.1016/j.jmb.2003.12.072
30-Sep-03     Release date:   01-Jun-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P56122  (AROC_HELPY) -  Chorismate synthase
365 a.a.
365 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Chorismate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Shikimate and Chorismate Biosynthesis
      Reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate
= chorismate
+ phosphate
      Cofactor: FMN
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular amino acid biosynthetic process   3 terms 
  Biochemical function     lyase activity     3 terms  


DOI no: 10.1016/j.jmb.2003.12.072 J Mol Biol 336:903-915 (2004)
PubMed id: 15095868  
Crystal structure of chorismate synthase: a novel FMN-binding protein fold and functional insights.
H.J.Ahn, H.J.Yoon, B.Lee, S.W.Suh.
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.
  Selected figure(s)  
Figure 4.
Figure 4. The active site and electron density of FMN. A, Electrostatic potential of the FMN-binding pocket. The positive electrostatic potential at the molecular surface of a monomer is colored in blue and the negative potential in red. Ten residues modeled as alanine are colored in dark yellow. FMN is shown in a stick model and colored in the same manner as in Figure 1A, except carbon atoms in white. B, Molecular surface of a chorismate synthase monomer covering the active site surrounded by six flexible regions. It is in the same orientation as in A. FMN is drawn in the same manner as in A. Strictly conserved residues and highly conserved residues on the molecular surface are colored in green and yellow, respectively. Each circle indicates six flexible regions, respectively. C, Stereo diagram of six flexible regions surrounding the active site in a tetramer. Only one of four active sites is emphasized. Thick traces denoting six flexible regions are colored as follows: F1 in cyan, F2 in green, F3 in yellow, F4 in red, F'5 in violet, and F6 in blue. F'5 is contributed from an adjacent subunit related by the Q-axis. Each monomer is colored in the same manner as in Figure 1A. D, Electron density of bound FMN. The 2F[o] -F[c] electron density map, contoured at 1.0s, is superimposed on the refined model. E, A view from the edge of the isoalloxazine ring, showing its significant non-planarity.
Figure 5.
Figure 5. FMN and EPSP-binding modes. A, Stereo diagram of FMN binding in the binary complex. FMN is drawn in a stick model and colored in the same manner as in Figure 1A, except carbon atoms in green. The residues interacting with FMN are also shown in stick models and colored in the same manner as in Figure 1A, except carbon atoms in light gray. Three red balls indicate water molecules. Black dotted lines represent hydrogen bonds. Purple dotted line denotes an ionic interaction between Lys244 and the phosphate group of FMN. The loops colored in light blue are from subunit A and the loop in light orange from the other subunit D, which is related by the Q-axis. Primed residue numbers denote that the residues come from the adjacent subunit. B, Stereo diagram of the FMN-EPSP-binding mode in the proposed model of the ternary complex. EPSP is colored in the same manner as FMN, except carbon atoms in yellow. Black and purple dotted lines are the same as in A. C, A schematic diagram of FMN binding in the binary complex. FMN is drawn in blue lines and three broken lines indicate three flexible loop regions F2, F4, and F6. Residues boxed in green color belong to subunit A and those in orange color to the other subunit D. Black and purple dotted lines are the same as in A. The reduced FMN is drawn in the mono-anionic form. D, A schematic diagram of the FMN-EPSP-binding mode in the proposed ternary complex model. EPSP is drawn in red lines. Black and purple dotted lines are the same as in A. Red dotted lines indicate interactions between FMN and EPSP that have been suggested by density functional calculations.[35.]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 336, 903-915) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19274093 D.Y.Little, and L.Chen (2009).
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
  PLoS ONE, 4, e4762.  
19735225 M.J.Duckworth, A.S.Okoli, and G.L.Mendz (2009).
Novel Helicobacter pylori therapeutic targets: the unusual suspects.
  Expert Rev Anti Infect Ther, 7, 835-867.  
18445278 F.Ely, J.E.Nunes, E.K.Schroeder, J.Frazzon, M.S.Palma, D.S.Santos, and L.A.Basso (2008).
The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthase.
  BMC Biochem, 9, 13.  
15937276 S.W.Aufhammer, E.Warkentin, U.Ermler, C.H.Hagemeier, R.K.Thauer, and S.Shima (2005).
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family.
  Protein Sci, 14, 1840-1849.
PDB code: 1z69
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.