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PDBsum entry 1pym

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protein ligands metals Protein-protein interface(s) links
Phosphotransferase PDB id
1pym
Jmol
Contents
Protein chains
291 a.a. *
Ligands
OXL ×2
Metals
_MG ×2
Waters ×590
* Residue conservation analysis
PDB id:
1pym
Name: Phosphotransferase
Title: Phosphoenolpyruvate mutase from mollusk in with bound mg2-ox
Structure: Protein (phosphoenolpyruvate mutase). Chain: a, b. Synonym: phosphoenolpyruvate phosphomutase. Engineered: yes. Other_details: with bound mg2+-oxalate inhibitor
Source: Mytilus edulis. Organism_taxid: 6550. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.80Å     R-factor:   0.188     R-free:   0.256
Authors: K.Huang,Z.Li,O.Herzberg
Key ref:
K.Huang et al. (1999). Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate. Structure, 7, 539-548. PubMed id: 10378273 DOI: 10.1016/S0969-2126(99)80070-7
Date:
25-Feb-99     Release date:   21-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56839  (PEPM_MYTED) -  Phosphoenolpyruvate phosphomutase
Seq:
Struc:
295 a.a.
291 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.4.2.9  - Phosphoenolpyruvate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Phosphoenolpyruvate Mutase
      Reaction: Phosphoenolpyruvate = 3-phosphonopyruvate
Phosphoenolpyruvate
Bound ligand (Het Group name = OXL)
matches with 45.45% similarity
= 3-phosphonopyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     organic phosphonate biosynthetic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(99)80070-7 Structure 7:539-548 (1999)
PubMed id: 10378273  
 
 
Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate.
K.Huang, Z.Li, Y.Jia, D.Dunaway-Mariano, O.Herzberg.
 
  ABSTRACT  
 
BACKGROUND: Phosphonate compounds are important secondary metabolites in nature and, when linked to macromolecules in eukaryotes, they might play a role in cell signaling. The first obligatory step in the biosynthesis of phosphonates is the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-pyr), a reaction that is catalyzed by PEP mutase. The PEP mutase functions as a tetramer and requires magnesium ions (Mg2+). RESULTS: The crystal structure of PEP mutase from the mollusk Mytilus edulis, bound to the inhibitor Mg(2+)-oxalate, has been determined using multiwavelength anomalous diffraction, exploiting the selenium absorption edge of a selenomethionine-containing protein. The structure has been refined at 1.8 A resolution. PEP mutase adopts a modified alpha/beta barrel fold, in which the eighth alpha helix projects away from the alpha/beta barrel instead of packing against the beta sheet. A tightly associated dimer is formed, such that the two eighth helices are swapped, each packing against the beta sheet of the neighboring molecule. A dimer of dimers further associates into a tetramer. Mg(2+)-oxalate is buried close to the center of the barrel, at the C-terminal ends of the beta strands. CONCLUSIONS: The tetramer observed in the crystal is likely to be physiologically relevant. Because the Mg(2+)-oxalate is inaccessible to solvent, substrate binding and dissociation might be accompanied by conformational changes. A mechanism involving a phosphoenzyme intermediate is proposed, with Asp58 acting as the nucleophilic entity that accepts and delivers the phosphoryl group. The active-site architecture and the chemistry performed by PEP mutase are different from other alpha/beta-barrel proteins that bind pyruvate or PEP, thus the enzyme might represent a new family of alpha/beta-barrel proteins.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Cartoon representation of ligand binding to four α/β-barrel PEP/pyruvate-utilizing enzymes. The β/α motifs are numbered sequentially. For PEP mutase, helix 8 is colored yellow because it is contributed by a neighboring molecule. The loop connecting the β/α motif 3 in pyruvate kinase corresponds to a whole domain and is shown as a broken yellow line. Motifs 1 and 2 in enolase do not obey the classical topology of β/α motifs. Residues that interact with PEP/pyruvate/oxalate are colored red. Residues that interact with Mg^2+ are colored blue.
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 539-548) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19489722 W.W.Metcalf, and W.A.van der Donk (2009).
Biosynthesis of phosphonic and phosphinic acid natural products.
  Annu Rev Biochem, 78, 65-94.  
19714241 Z.Diaz, K.B.Xavier, and S.T.Miller (2009).
The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
  PLoS One, 4, e6820.
PDB codes: 3gkf 3glc 3gnd
18081320 B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, and O.Herzberg (2008).
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
  Biochemistry, 47, 167-182.
PDB code: 3b8i
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
17244616 Y.Han, H.J.Joosten, W.Niu, Z.Zhao, P.S.Mariano, M.McCalman, J.van Kan, P.J.Schaap, and D.Dunaway-Mariano (2007).
Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi.
  J Biol Chem, 282, 9581-9590.  
14747998 B.Japelj, J.P.Waltho, and R.Jerala (2004).
Comparison of backbone dynamics of monomeric and domain-swapped stefin A.
  Proteins, 54, 500-512.  
15213379 T.Ose, K.Watanabe, M.Yao, M.Honma, H.Oikawa, and I.Tanaka (2004).
Structure of macrophomate synthase.
  Acta Crystallogr D Biol Crystallogr, 60, 1187-1197.  
12842039 B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, and T.O.Yeates (2003).
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
  Structure, 11, 753-764.
PDB code: 1oy0
12906829 F.von Delft, T.Inoue, S.A.Saldanha, H.H.Ottenhof, F.Schmitzberger, L.M.Birch, V.Dhanaraj, M.Witty, A.G.Smith, T.L.Blundell, and C.Abell (2003).
Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites.
  Structure, 11, 985-996.
PDB code: 1m3u
12672809 M.Sarkar, C.J.Hamilton, and A.H.Fairlamb (2003).
Properties of phosphoenolpyruvate mutase, the first enzyme in the aminoethylphosphonate biosynthetic pathway in Trypanosoma cruzi.
  J Biol Chem, 278, 22703-22708.  
11741915 L.F.Garcia-Alles, K.Flükiger, J.Hewel, R.Gutknecht, C.Siebold, S.Schürch, and B.Erni (2002).
Mechanism-based inhibition of enzyme I of the Escherichia coli phosphotransferase system. Cysteine 502 is an essential residue.
  J Biol Chem, 277, 6934-6942.  
12162742 S.Liu, Z.Lu, Y.Jia, D.Dunaway-Mariano, and O.Herzberg (2002).
Dissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants.
  Biochemistry, 41, 10270-10276.
PDB code: 1m1b
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11526312 K.L.Britton, I.S.Abeysinghe, P.J.Baker, V.Barynin, P.Diehl, S.J.Langridge, B.A.McFadden, S.E.Sedelnikova, T.J.Stillman, K.Weeradechapon, and D.W.Rice (2001).
The structure and domain organization of Escherichia coli isocitrate lyase.
  Acta Crystallogr D Biol Crystallogr, 57, 1209-1218.
PDB code: 1igw
10801489 K.Britton, S.Langridge, P.J.Baker, K.Weeradechapon, S.E.Sedelnikova, J.R.De Lucas, D.W.Rice, and G.Turner (2000).
The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
  Structure, 8, 349-362.
PDB code: 1dqu
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.