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PDBsum entry 1q36

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protein ligands links
Transferase PDB id
1q36
Jmol
Contents
Protein chain
427 a.a. *
Ligands
SKP
FMT ×9
Waters ×539
* Residue conservation analysis
PDB id:
1q36
Name: Transferase
Title: Epsp synthase (asp313ala) liganded with tetrahedral reaction intermediate
Structure: 3-phosphoshikimate 1-carboxyvinyltransferase. Chain: a. Synonym: 5-enolpyruvylshikimate-3-phosphate synthase, epsp synthase, epsps. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: aroa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.155     R-free:   0.187
Authors: S.Eschenburg,W.Kabsch,M.L.Healy,E.Schonbrunn
Key ref:
S.Eschenburg et al. (2003). A new view of the mechanisms of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) derived from X-ray structures of their tetrahedral reaction intermediate states. J Biol Chem, 278, 49215-49222. PubMed id: 13129913 DOI: 10.1074/jbc.M309741200
Date:
28-Jul-03     Release date:   16-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A6D3  (AROA_ECOLI) -  3-phosphoshikimate 1-carboxyvinyltransferase
Seq:
Struc:
427 a.a.
427 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.19  - 3-phosphoshikimate 1-carboxyvinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Shikimate and Chorismate Biosynthesis
      Reaction: Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O- (1-carboxyvinyl)-3-phosphoshikimate
Phosphoenolpyruvate
+ 3-phosphoshikimate
= phosphate
+
5-O- (1-carboxyvinyl)-3-phosphoshikimate
Bound ligand (Het Group name = SKP)
matches with 80.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular amino acid biosynthetic process   3 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M309741200 J Biol Chem 278:49215-49222 (2003)
PubMed id: 13129913  
 
 
A new view of the mechanisms of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) derived from X-ray structures of their tetrahedral reaction intermediate states.
S.Eschenburg, W.Kabsch, M.L.Healy, E.Schonbrunn.
 
  ABSTRACT  
 
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) constitute the small enzyme family of enolpyruvyl transferases, which catalyze the chemically unusual reaction of enolpyruvyl transfer. MurA catalyzes the first step in the biosynthesis of the bacterial cell wall; AroA is the sixth enzyme of the shikimate pathway leading to the synthesis of aromatic compounds in numerous microorganisms and plants. Because both metabolic pathways are absent from mammals but essential for the growth of microorganisms, MurA and AroA are attractive targets for the development of novel antimicrobial drugs. We have determined the x-ray structures of the D305A mutant of Enterobacter cloacae MurA and the D313A mutant of Escherichia coli AroA, both of which crystallized in the presence of their substrates. The structures depict the tetrahedral reaction intermediate states of the enzymes and prove that, without the aspartate side chain, the overall addition-elimination reaction in both enzymes is halted after the addition step. The presented structures lead to a new view of the catalytic mechanism and, moreover, provide an ideal starting point for the rational design of potent inhibitors of MurA and AroA.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. The addition-elimination mechanism of enolpyruvyl transferases. The designations enzyme-X, enzyme-Y, and Z-enzyme stand for side chains involved in the transfer reaction. A proton is added to PEP, yielding a PEP oxocarbenium ion, while the target hydroxyl group of the first bound substrate, S1 (UNAG and S3P for MurA and AroA, respectively), gets deprotonated (A). A nucleophilic attack of the deprotonated target hydroxyl group of S1 on the C-2 atom of the PEP oxocarbenium ion (B) leads to a covalent adduct of the two substrates where the C-2 atom of the PEP moiety is in tetrahedral configuration (C). Subtraction of a proton from the methyl group at C-3 of the PEP moiety (D) results in the formation of the vinyl ether product under elimination of inorganic phosphate (E).
Figure 5.
FIG. 5. Comparison of the tetrahedral intermediate states of the enolpyruvyl transfer reactions in D305A-MurA and D313A-AroA. Top stereo pair, active site of MurA. Middle stereo pair, active site of AroA. The tetrahedral adducts are shown in green, and the set of charged residues common to MurA and AroA is highlighted in magenta. The aspartate side chain in position 305/313 is adumbrated as derived from homology modeling. Polar or charged interactions are denoted by dashed lines. Close to Trp-95 in MurA an ethylene glycol molecule is bound, which stems from the cryoprotectant solution. Bottom stereo pair, superposition of the active sites of MurA (reddish colors, magenta labels) and AroA (greenish colors, blue labels), with the chiral center at the C-2 atom of PEP as reference.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 49215-49222) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179877 P.Domínguez de María, R.W.van Gemert, A.J.Straathof, and U.Hanefeld (2010).
Biosynthesis of ethers: unusual or common natural events?
  Nat Prod Rep, 27, 370-392.  
19298367 K.L.Blake, A.J.O'Neill, D.Mengin-Lecreulx, P.J.Henderson, J.M.Bostock, C.J.Dunsmore, K.J.Simmons, C.W.Fishwick, J.A.Leeds, and I.Chopra (2009).
The nature of Staphylococcus aureus MurA and MurZ and approaches for detection of peptidoglycan biosynthesis inhibitors.
  Mol Microbiol, 72, 335-343.  
19211556 T.Funke, Y.Yang, H.Han, M.Healy-Fried, S.Olesen, A.Becker, and E.Schönbrunn (2009).
Structural basis of glyphosate resistance resulting from the double mutation Thr97 -> Ile and Pro101 -> Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli.
  J Biol Chem, 284, 9854-9860.
PDB codes: 3fjx 3fjz 3fk0 3fk1
18310348 A.Sebkova, D.Karasova, M.Crhanova, E.Budinska, and I.Rychlik (2008).
aro mutations in Salmonella enterica cause defects in cell wall and outer membrane integrity.
  J Bacteriol, 190, 3155-3160.  
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
17124631 C.D.Klein, and A.Bachelier (2006).
Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective.
  J Comput Aided Mol Des, 20, 621-628.  
16978018 D.K.Nomura, K.A.Durkin, K.P.Chiang, G.B.Quistad, B.F.Cravatt, and J.E.Casida (2006).
Serine hydrolase KIAA1363: toxicological and structural features with emphasis on organophosphate interactions.
  Chem Res Toxicol, 19, 1142-1150.  
16916934 T.Funke, H.Han, M.L.Healy-Fried, M.Fischer, and E.Schönbrunn (2006).
Molecular basis for the herbicide resistance of Roundup Ready crops.
  Proc Natl Acad Sci U S A, 103, 13010-13015.
PDB codes: 2gg4 2gg6 2gga 2ggd
16304142 J.G.Hurdle, A.J.O'Neill, and I.Chopra (2005).
Prospects for aminoacyl-tRNA synthetase inhibitors as new antimicrobial agents.
  Antimicrob Agents Chemother, 49, 4821-4833.  
16085874 Y.C.Sun, Y.C.Chen, Z.X.Tian, F.M.Li, X.Y.Wang, J.Zhang, Z.L.Xiao, M.Lin, N.Gilmartin, D.N.Dowling, and Y.P.Wang (2005).
Novel AroA with high tolerance to glyphosate, encoded by a gene of Pseudomonas putida 4G-1 isolated from an extremely polluted environment in China.
  Appl Environ Microbiol, 71, 4771-4776.  
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 codes are shown on the right.