PDBsum entry 1m1b

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Isomerase PDB id
Protein chains
291 a.a. *
SPV ×2
_MG ×2
Waters ×257
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of phosphoenolpyruvate mutase complexed wi sulfopyruvate
Structure: Phosphoenolpyruvate phosphomutase. Chain: a, b. Synonym: phosphoenolpyruvate mutase, pep mutase, pep phosph engineered: yes
Source: Mytilus edulis. Organism_taxid: 6550. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
2.25Å     R-factor:   0.179     R-free:   0.268
Authors: S.Liu,Z.Lu,Y.Jia,D.Dunaway-Mariano,O.Herzberg
Key ref:
S.Liu et al. (2002). Dissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants. Biochemistry, 41, 10270-10276. PubMed id: 12162742 DOI: 10.1021/bi026024v
18-Jun-02     Release date:   28-Aug-02    
Go to PROCHECK summary

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

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

Phosphoenolpyruvate Mutase
      Reaction: Phosphoenolpyruvate = 3-phosphonopyruvate
Bound ligand (Het Group name = SPV)
matches with 42.86% 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: 10.1021/bi026024v Biochemistry 41:10270-10276 (2002)
PubMed id: 12162742  
Dissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants.
S.Liu, Z.Lu, Y.Jia, D.Dunaway-Mariano, O.Herzberg.
The crystal structure of PEP mutase from Mytilus edulis in complex with a substrate-analogue inhibitor, sulfopyruvate S-pyr (K(i) = 22 microM), has been determined at 2.25 A resolution. Mg(II)-S-pyr binds in the alpha/beta barrel's central channel, at the C-termini of the beta-strands. The binding mode of S-pyr's pyruvyl moiety resembles the binding mode of oxalate seen earlier. The location of the sulfo group of S-pyr is postulated to mimic the phosphonyl group of the product phosphonopyruvate (P-pyr). This sulfo group interacts with the guanidinium group of Arg159, but it is not aligned for nucleopilic attack by neighboring basic amino side chains. Kinetic analysis of site directed mutants, probing the key active site residues Asp58, Arg159, Asn122, and His190 correlate well with the structural information. The results presented here rule out a phosphoryl transfer mechanism involving a double displacement, and suggest instead that PEP mutase catalysis proceeds via a dissociative mechanism in which the pyruvyl C(3) adds to the same face of the phosphorus from which the C(2)O departs. We propose that Arg159 and His190 serve to hold the phosphoryl/metaphosphate/phosphonyl group stationary along the reaction pathway, while the pyruvyl C(1)-C(2) bond rotates upon formation of the metaphosphate. In agreement with published data, the phosphoryl group transfer occurs on the Si-face of PEP with retention of configuration at phosphorus.

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.  
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
18656958 J.W.Munos, S.J.Moon, S.O.Mansoorabadi, W.Chang, L.Hong, F.Yan, A.Liu, and H.W.Liu (2008).
Purification and characterization of the epoxidase catalyzing the formation of fosfomycin from Pseudomonas syringae.
  Biochemistry, 47, 8726-8735.  
17283804 I.Ntai, V.V.Phelan, and B.O.Bachmann (2006).
Phosphonopeptide K-26 biosynthetic intermediates in Astrosporangium hypotensionis.
  Chem Commun (Camb), (), 4518-4520.  
16433548 J.G.Zalatan, and D.Herschlag (2006).
Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.
  J Am Chem Soc, 128, 1293-1303.  
12904299 G.Zhang, J.Dai, Z.Lu, and D.Dunaway-Mariano (2003).
The phosphonopyruvate decarboxylase from Bacteroides fragilis.
  J Biol Chem, 278, 41302-41308.  
14529267 P.Liu, A.Liu, F.Yan, M.D.Wolfe, J.D.Lipscomb, and H.W.Liu (2003).
Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme.
  Biochemistry, 42, 11577-11586.  
12897003 T.L.Grimek, H.Holden, I.Rayment, and J.C.Escalante-Semerena (2003).
Residues C123 and D58 of the 2-methylisocitrate lyase (PrpB) enzyme of Salmonella enterica are essential for catalysis.
  J Bacteriol, 185, 4837-4843.  
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.