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PDBsum entry 1eyn

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Transferase PDB id
1eyn
Jmol
Contents
Protein chain
419 a.a. *
Ligands
2AN
GOL ×2
Waters ×506
* Residue conservation analysis
PDB id:
1eyn
Name: Transferase
Title: Structure of mura liganded with the extrinsic fluorescence p
Structure: Udp-n-acetylglucosamine 1-carboxyvinyltransferase chain: a. Synonym: enoylpyruvate transferase, ept, mura. Engineered: yes. Mutation: yes
Source: Enterobacter cloacae. Organism_taxid: 550. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.70Å     R-factor:   0.180     R-free:   0.210
Authors: E.Schonbrunn,S.Eschenburg,K.Luger,W.Kabsch,N.Amrhein
Key ref:
E.Schonbrunn et al. (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. PubMed id: 10823915 DOI: 10.1073/pnas.120120397
Date:
07-May-00     Release date:   09-Jun-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P33038  (MURA_ENTCC) -  UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Seq:
Struc:
419 a.a.
419 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
Bound ligand (Het Group name = GOL)
matches with 45.45% similarity
+ UDP-N-acetyl-alpha-D-glucosamine
= phosphate
+ UDP- N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine
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: 10.1073/pnas.120120397 Proc Natl Acad Sci U S A 97:6345-6349 (2000)
PubMed id: 10823915  
 
 
Structural basis for the interaction of the fluorescence probe 8-anilino-1-naphthalene sulfonate (ANS) with the antibiotic target MurA.
E.Schonbrunn, S.Eschenburg, K.Luger, W.Kabsch, N.Amrhein.
 
  ABSTRACT  
 
The extrinsic fluorescence dye 8-anilino-1-naphthalene sulfonate (ANS) is widely used for probing conformational changes in proteins, yet no detailed structure of ANS bound to any protein has been reported so far. ANS has been successfully used to monitor the induced-fit mechanism of MurA [UDPGlcNAc enolpyruvyltransferase (EC )], an essential enzyme for bacterial cell wall biosynthesis. We have solved the crystal structure of the ANS small middle dotMurA complex at 1.7-A resolution. ANS binds at an originally solvent-exposed region near Pro-112 and induces a major restructuring of the loop Pro-112-Pro-121, such that a specific binding site emerges. The fluorescence probe is sandwiched between the strictly conserved residues Arg-91, Pro-112, and Gly-113. Substrate binding to MurA is accompanied by large movements especially of the loop and Arg-91, which explains why ANS is an excellent sensor of conformational changes during catalysis of this pharmaceutically important enzyme.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. The ANS binding site in MurA. (Upper) Representation of the F[o] F[c] difference density contoured at 3 in the region of the ANS binding site. ANS was omitted in the refinement and the calculation of the Fourier synthesis. (Lower) The final 2F[o] F[c] electron density contoured at 1 . ANS was included in the refinement and the calculation of the Fourier synthesis. Carbon atoms are colored yellow, nitrogen atoms blue, oxygen atoms red, sulfur atoms green. Solvent molecules are shown as red spheres. Thick dashed lines represent hydrogen bonds. To designate hydrophobic interactions, distances between ring centers and closest carbon atoms are given along thin dashed lines. The figure was drawn with BOBSCRIPT (22).
Figure 4.
Fig. 4. Conformational changes in the loop around Cys-115. Stereo representations of the loop in unliganded MurA[type2] (11) (A), ANS-liganded MurA (B), and the closed state of MurA (7) (C). Arg-91 (yellow), the ANS molecule (orange), and the main chain of the loop Pro-112-Gly-Gly-Cys-Ala-Ile-Gly-Ala-Arg-Pro-121 together with the side chains of Pro-112, Cys-115, and Pro-121 (magenta) are represented as ball and stick. Noncarbon atoms are color-coded as in Fig. 3. Turquoise spheres and dashed lines designate water molecules and hydrogen bonds, respectively. The surrounding protein is shown as a gray -carbon trace. The view corresponds to a zoom of Fig. 2. The structures were aligned through residues Asp-231, Asp-305, Arg-371, and Arg-331 of the bottom domain of MurA.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205172 C.L.Wang, and H.L.Yang (2011).
Conserved residues in the subunit interface of tau glutathione s-transferase affect catalytic and structural functions.
  J Integr Plant Biol, 53, 35-43.  
20687233 M.Andujar-Sánchez, V.Jara-Perez, E.S.Cobos, and A.Cámara-Artigas (2011).
A thermodynamic characterization of the interaction of 8-anilino-1-naphthalenesulfonic acid with native globular proteins: the effect of the ligand dimerization in the analysis of the binding isotherms.
  J Mol Recognit, 24, 548-556.  
19651777 A.Tiwari, A.Liba, S.H.Sohn, S.V.Seetharaman, O.Bilsel, C.R.Matthews, P.J.Hart, J.S.Valentine, and L.J.Hayward (2009).
Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis.
  J Biol Chem, 284, 27746-27758.  
18953685 G.D.Markham, and M.A.Pajares (2009).
Structure-function relationships in methionine adenosyltransferases.
  Cell Mol Life Sci, 66, 636-648.  
17729272 C.S.Cheng, M.N.Chen, Y.T.Lai, T.Chen, K.F.Lin, Y.J.Liu, and P.C.Lyu (2008).
Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding.
  Proteins, 70, 695-706.  
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.  
18703268 N.Kinsley, Y.Sayed, S.Mosebi, R.N.Armstrong, and H.W.Dirr (2008).
Characterization of the binding of 8-anilinonaphthalene sulfonate to rat class Mu GST M1-1.
  Biophys Chem, 137, 100-104.  
17180467 M.Jokiel, D.Shcharbin, J.Janiszewska, Z.Urbanczyk-Lipkowska, and M.Bryszewska (2007).
The interaction between polycationic poly-lysine dendrimers and charged and neutral fluorescent probes.
  J Fluoresc, 17, 73-79.  
18028215 O.K.Gasymov, A.R.Abduragimov, and B.J.Glasgow (2007).
Characterization of fluorescence of ANS-tear lipocalin complex: evidence for multiple-binding modes.
  Photochem Photobiol, 83, 1405-1414.  
17321809 O.K.Gasymov, and B.J.Glasgow (2007).
ANS fluorescence: potential to augment the identification of the external binding sites of proteins.
  Biochim Biophys Acta, 1774, 403-411.  
18000547 U.Das, G.Hariprasad, A.S.Ethayathulla, P.Manral, T.K.Das, S.Pasha, A.Mann, M.Ganguli, A.K.Verma, R.Bhat, S.K.Chandrayan, S.Ahmed, S.Sharma, P.Kaur, T.P.Singh, and A.Srinivasan (2007).
Inhibition of protein aggregation: supramolecular assemblies of arginine hold the key.
  PLoS ONE, 2, e1176.  
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.  
16401611 M.K.Smalley, and S.K.Silverman (2006).
Fluorescence of covalently attached pyrene as a general RNA folding probe.
  Nucleic Acids Res, 34, 152-166.  
16964599 S.Pedersen, L.Nesgaard, R.P.Baptista, E.P.Melo, S.R.Kristensen, and D.E.Otzen (2006).
pH-dependent aggregation of cutinase is efficiently suppressed by 1,8-ANS.
  Biopolymers, 83, 619-629.  
11847284 C.D.Smith, M.Carson, A.M.Friedman, M.M.Skinner, L.Delucas, L.Chantalat, L.Weise, T.Shirasawa, and D.Chattopadhyay (2002).
Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.
  Protein Sci, 11, 625-635.
PDB code: 1i1n
11901475 D.W.Green (2002).
The bacterial cell wall as a source of antibacterial targets.
  Expert Opin Ther Targets, 6, 1.  
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.  
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.