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PDBsum entry 1a2n

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Transferase PDB id
1a2n
Jmol
Contents
Protein chain
418 a.a. *
Ligands
TET
Waters ×271
* Residue conservation analysis
PDB id:
1a2n
Name: Transferase
Title: Structure of the c115a mutant of mura complexed with the fluorinated analog of the reaction tetrahedral intermediate
Structure: Udp-n-acetylglucosamine enolpyruvyl transferase. Chain: a. Synonym: mura. Engineered: yes. Mutation: yes. Other_details: ligand is the fluorinated analog of the reaction tetrahedral intermediate
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
2.80Å     R-factor:   0.175    
Authors: T.Skarzynski
Key ref:
T.Skarzynski et al. (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. PubMed id: 9485407 DOI: 10.1021/bi9722608
Date:
06-Jan-98     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A749  (MURA_ECOLI) -  UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Seq:
Struc:
419 a.a.
418 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.2.5.1.7  - UDP-N-acetylglucosamine 1-carboxyvinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Peptidoglycan Biosynthesis (Part 1)
      Reaction: Phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP- N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine
Phosphoenolpyruvate
+ UDP-N-acetyl-alpha-D-glucosamine
= phosphate
+ UDP- N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine
Bound ligand (Het Group name = TET)
matches with 88.00% 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     cell wall organization   6 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9722608 Biochemistry 37:2572-2577 (1998)
PubMed id: 9485407  
 
 
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.
T.Skarzynski, D.H.Kim, W.J.Lees, C.T.Walsh, K.Duncan.
 
  ABSTRACT  
 
MurA (UDP-GlcNAc enolpyruvyl transferase), the first enzyme in bacterial peptidoglycan biosynthesis, catalyzes the enolpyruvyl transfer from phosphoenolpyruvate (PEP) to the 3'-OH of UDP-GlcNAc by an addition-elimination mechanism that proceeds through a tetrahedral ketal intermediate. The crystal structure of the Cys115-to-Ala (C115A) mutant of Escherichia coli MurA complexed with a fluoro analogue of the tetrahedral intermediate revealed the absolute configuration of the adduct and the stereochemical course of the reaction. The fluorinated adduct was generated in a preincubation of wild-type MurA with (Z)-3-fluorophosphoenolpyruvate (FPEP) and UDP-GlcNAc and purified after enzyme denaturation. The fluorine substituent stabilizes the tetrahedral intermediate toward decomposition by a factor of 10(4)-10(6), facilitating manipulation of the adduct. The C115A mutant of MurA was utilized to avoid the microheterogeneity that arises in the wild-type MurA from the attack of Cys115 on C-2 of FPEP in competition with the formation of the fluorinated adduct. The crystal structure of the complex was determined to 2.8 A resolution, and the absolute configuration at C-2 of the adduct was found to be 2R. Thus, addition of the 3'-OH of UDP-GlcNAc is to the 2-si face of FPEP, corresponding to the 2-re face of PEP. Given the previous observation that, in D2O, the addition of D+ to C-3 of PEP proceeds from the 2-si face [Kim, D. H., Lees, W. J., and Walsh, C. T. (1995) J. Am. Chem. Soc. 117, 6380-6381], the addition across the double bond of PEP is anti. Also, because the overall stereochemical course has been shown to be either anti/syn or syn/anti [Lees, W. J., and Walsh, C. T. (1995) J. Am. Chem. Soc. 117, 7329-7337], it now follows that the stereochemistry of elimination of H+ from C-3 and Pi from C-2 of the tetrahedral intermediate of the reaction is syn.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18247346 H.J.Yoon, S.J.Lee, B.Mikami, H.J.Park, J.Yoo, and S.W.Suh (2008).
Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin.
  Proteins, 71, 1032-1037.
PDB codes: 2rl1 2rl2
18171026 J.P.Alexander, T.J.Ryan, D.P.Ballou, and J.K.Coward (2008).
Gamma-glutamyl hydrolase: kinetic characterization of isopeptide hydrolysis using fluorogenic substrates.
  Biochemistry, 47, 1228-1239.  
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.  
15531591 S.Eschenburg, M.Priestman, and E.Schönbrunn (2005).
Evidence that the fosfomycin target Cys115 in UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is essential for product release.
  J Biol Chem, 280, 3757-3763.
PDB code: 1ryw
15206933 A.M.Thomas, C.Ginj, I.Jelesarov, N.Amrhein, and P.Macheroux (2004).
Role of K22 and R120 in the covalent binding of the antibiotic fosfomycin and the substrate-induced conformational change in UDP-N-acetylglucosamine enolpyruvyl transferase.
  Eur J Biochem, 271, 2682-2690.  
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
12492849 A.El Zoeiby, F.Sanschagrin, and R.C.Levesque (2003).
Structure and function of the Mur enzymes: development of novel inhibitors.
  Mol Microbiol, 47, 1.  
13129913 S.Eschenburg, W.Kabsch, M.L.Healy, and E.Schonbrunn (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.
PDB codes: 1q36 1q3g
11901475 D.W.Green (2002).
The bacterial cell wall as a source of antibacterial targets.
  Expert Opin Ther Targets, 6, 1.  
11327813 A.K.Samland, T.Etezady-Esfarjani, N.Amrhein, and P.Macheroux (2001).
Asparagine 23 and aspartate 305 are essential residues in the active site of UDP-N-acetylglucosamine enolpyruvyl transferase from Enterobacter cloacae.
  Biochemistry, 40, 1550-1559.  
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
10694381 E.Schönbrunn, S.Eschenburg, F.Krekel, K.Luger, and N.Amrhein (2000).
Role of the loop containing residue 115 in the induced-fit mechanism of the bacterial cell wall biosynthetic enzyme MurA.
  Biochemistry, 39, 2164-2173.
PDB code: 1dlg
11027147 F.Krekel, A.K.Samland, P.Macheroux, N.Amrhein, and J.N.Evans (2000).
Determination of the pKa value of C115 in MurA (UDP-N-acetylglucosamine enolpyruvyltransferase) from Enterobacter cloacae.
  Biochemistry, 39, 12671-12677.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10842342 S.Eschenburg, and E.Schönbrunn (2000).
Comparative X-ray analysis of the un-liganded fosfomycin-target murA.
  Proteins, 40, 290-298.
PDB codes: 1ejc 1ejd
10413459 F.Krekel, C.Oecking, N.Amrhein, and P.Macheroux (1999).
Substrate and inhibitor-induced conformational changes in the structurally related enzymes UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS).
  Biochemistry, 38, 8864-8878.  
9724511 D.L.Jakeman, D.J.Mitchell, W.A.Shuttleworth, and J.N.Evans (1998).
On the mechanism of 5-enolpyruvylshikimate-3-phosphate synthase.
  Biochemistry, 37, 12012-12019.  
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.