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Transferase PDB id
1eps
Jmol
Contents
Protein chain
427 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1eps
Name: Transferase
Title: Structure and topological symmetry of the glyphosphate 5- enol-pyruvylshikimate-3-phosphate synthase: a distinctive protein fold
Structure: 5-enol-pyruvyl-3-phosphate synthase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Resolution:
3.00Å     R-factor:   not given    
Authors: W.C.Stallings,S.S.Abdel-Meguid,L.W.Lim,H.-S.Shieh, H.E.Dayringer,N.K.Leimgruber,R.A.Stegeman,K.S.Anderson, J.A.Sikorski,S.R.Padgette,G.M.Kishore
Key ref: W.C.Stallings et al. (1991). Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold. Proc Natl Acad Sci U S A, 88, 5046-5050. PubMed id: 11607190 DOI: 10.1073/pnas.88.11.5046
Date:
05-Apr-91     Release date:   15-Jul-93    
 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
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
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   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.88.11.5046 Proc Natl Acad Sci U S A 88:5046-5050 (1991)
PubMed id: 11607190  
 
 
Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold.
W.C.Stallings, S.S.Abdel-Meguid, L.W.Lim, H.S.Shieh, H.E.Dayringer, N.K.Leimgruber, R.A.Stegeman, K.S.Anderson, J.A.Sikorski, S.R.Padgette, G.M.Kishore.
 
  ABSTRACT  
 
5-enol-Pyruvylshikimate-3-phosphate synthase (EPSP synthase; phosphoenolpyruvate:3-phosphoshikimate 1-carboxyvinyltransferase, EC 2.5.1.19) is an enzyme on the pathway toward the synthesis of aromatic amino acids in plants, fungi, and bacteria and is the target of the broad-spectrum herbicide glyphosate. The three-dimensional structure of the enzyme from Escherichia coli has been determined by crystallographic techniques. The polypeptide backbone chain was traced by examination of an electron density map calculated at 3-A resolution. The two-domain structure has a distinctive fold and appears to be formed by 6-fold replication of a protein folding unit comprising two parallel helices and a four-stranded sheet. Each domain is formed from three of these units, which are related by an approximate threefold symmetry axis; in each domain three of the helices are completely buried by a surface formed from the three beta-sheets and solvent-accessible faces of the other three helices. The domains are related by an approximate dyad, but in the present crystals the molecule does not display pseudo-symmetry related to the symmetry of point group 32 because its approximate threefold axes are almost normal. A possible relation between the three-dimensional structure of the protein and the linear sequence of its gene will be described. The topological threefold symmetry and orientation of each of the two observed globular domains may direct the binding of substrates and inhibitors by a helix macrodipole effect and implies that the active site is located near the interdomain crossover segments. The structure also suggests a rationale for the glyphosate tolerance conferred by sequence alterations.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19043750 G.B.Barcellos, R.A.Caceres, and W.F.de Azevedo (2009).
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.
  J Mol Model, 15, 147-155.  
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
16293685 P.C.Feng, G.J.Baley, W.P.Clinton, G.J.Bunkers, M.F.Alibhai, T.C.Paulitz, and K.K.Kidwell (2005).
Glyphosate inhibits rust diseases in glyphosate-resistant wheat and soybean.
  Proc Natl Acad Sci U S A, 102, 17290-17295.  
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.  
14763973 H.Park, J.L.Hilsenbeck, H.J.Kim, W.A.Shuttleworth, Y.H.Park, J.N.Evans, and C.Kang (2004).
Structural studies of Streptococcus pneumoniae EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3P-GLP-bound state.
  Mol Microbiol, 51, 963-971.
PDB codes: 1rf4 1rf5 1rf6
  12906831 A.K.Padyana, and S.K.Burley (2003).
Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
  Structure, 11, 1005-1013.
PDB code: 1nvt
  14656434 J.Maclean, and S.Ali (2003).
The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction.
  Structure, 11, 1499-1511.
PDB code: 1qxo
12843673 M.He, Y.F.Nie, and P.Xu (2003).
A T42M substitution in bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) generates enzymes with increased resistance to glyphosate.
  Biosci Biotechnol Biochem, 67, 1405-1409.  
12112685 C.Watts, S.M.Si-Hoe, H.K.Lamb, L.J.Levett, J.R.Coggins, and A.R.Hawkins (2002).
Kinetic analysis of the interaction between the QutA and QutR transcription-regulating proteins.
  Proteins, 48, 161-168.  
11171958 E.Schönbrunn, S.Eschenburg, W.A.Shuttleworth, J.V.Schloss, N.Amrhein, J.N.Evans, and W.Kabsch (2001).
Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail.
  Proc Natl Acad Sci U S A, 98, 1376-1380.
PDB codes: 1g6s 1g6t
11248008 M.F.Alibhai, and W.C.Stallings (2001).
Closing down on glyphosate inhibition--with a new structure for drug discovery.
  Proc Natl Acad Sci U S A, 98, 2944-2946.  
10823915 E.Schonbrunn, S.Eschenburg, K.Luger, W.Kabsch, and N.Amrhein (2000).
Structural basis for the interaction of the fluorescence probe 8-anilino-1-naphthalene sulfonate (ANS) with the antibiotic target MurA.
  Proc Natl Acad Sci U S A, 97, 6345-6349.
PDB code: 1eyn
  10673421 G.J.Palm, E.Billy, W.Filipowicz, and A.Wlodawer (2000).
Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology.
  Structure, 8, 13-23.
PDB codes: 1qmh 1qmi
15012217 K.M.Herrmann, and L.M.Weaver (1999).
THE SHIKIMATE PATHWAY.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 473-503.  
9485407 T.Skarzynski, D.H.Kim, W.J.Lees, C.T.Walsh, and K.Duncan (1998).
Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral intermediate bound to the active site of the C115A mutant of MurA.
  Biochemistry, 37, 2572-2577.
PDB code: 1a2n
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  8805594 C.Davies, V.Ramakrishnan, and S.W.White (1996).
Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution.
  Structure, 4, 1093-1104.
PDB code: 1sei
  8805592 E.Schönbrunn, S.Sack, S.Eschenburg, A.Perrakis, F.Krekel, N.Amrhein, and E.Mandelkow (1996).
Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin.
  Structure, 4, 1065-1075.
PDB code: 1naw
  8994972 T.Skarzynski, A.Mistry, A.Wonacott, S.E.Hutchinson, V.A.Kelly, and K.Duncan (1996).
Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin.
  Structure, 4, 1465-1474.
PDB code: 1uae
7556173 A.R.Hawkins, and H.K.Lamb (1995).
The molecular biology of multidomain proteins. Selected examples.
  Eur J Biochem, 232, 7.  
8281938 C.Wanke, and N.Amrhein (1993).
Evidence that the reaction of the UDP-N-acetylglucosamine 1-carboxyvinyltransferase proceeds through the O-phosphothioketal of pyruvic acid bound to Cys115 of the enzyme.
  Eur J Biochem, 218, 861-870.  
  1512209 J.L.Marquardt, D.A.Siegele, R.Kolter, and C.T.Walsh (1992).
Cloning and sequencing of Escherichia coli murZ and purification of its product, a UDP-N-acetylglucosamine enolpyruvyl transferase.
  J Bacteriol, 174, 5748-5752.  
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.