PDBsum entry 1ejj

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Isomerase PDB id
Protein chain
508 a.a. *
_MN ×2
Waters ×180
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structural analysis of phosphoglycerate mutase cocrystallized with 3-phosphoglycerate
Structure: Phosphoglycerate mutase. Chain: a. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
1.90Å     R-factor:   0.207     R-free:   0.247
Authors: M.J.Jedrzejas,M.Chander,P.Setlow,G.Krishnasamy
Key ref:
M.J.Jedrzejas et al. (2000). Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J, 19, 1419-1431. PubMed id: 10747010 DOI: 10.1093/emboj/19.7.1419
02-Mar-00     Release date:   02-Mar-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9X519  (GPMI_GEOSE) -  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
511 a.a.
508 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
Bound ligand (Het Group name = 3PG)
corresponds exactly
      Cofactor: Cobalt cation or Mn(2+)
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     metabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  


    Added reference    
DOI no: 10.1093/emboj/19.7.1419 EMBO J 19:1419-1431 (2000)
PubMed id: 10747010  
Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus.
M.J.Jedrzejas, M.Chander, P.Setlow, G.Krishnasamy.
Bacillus stearothermophilus phosphoglycerate mutase (PGM), which interconverts 2- and 3-phosphoglyceric acid (PGA), does not require 2,3-diphosphoglyceric acid for activity. However, this enzyme does have an absolute and specific requirement for Mn(2+) ions for catalysis. Here we report the crystal structure of this enzyme complexed with 3PGA and manganese ions to 1.9 A resolution; this is the first crystal structure of a diphosphoglycerate-independent PGM to be determined. This information, plus the location of the two bound Mn(2+) ions and the 3PGA have allowed formulation of a possible catalytic mechanism for this PGM. In this mechanism Mn(2+) ions facilitate the transfer of the substrate's phosphate group to Ser62 to form a phosphoserine intermediate. In the subsequent phosphotransferase part of the reaction, the phosphate group is transferred from Ser62 to the O2 or O3 positions of the reoriented glycerate to yield the PGA product. Site-directed mutagenesis studies were used to confirm our mechanism and the involvement of specific enzyme residues in Mn(2+) binding and catalysis.
  Selected figure(s)  
Figure 3.
Figure 3 (A) The interaction of active site residues with the 3PGA substrate and Mn^2+ ions. A total of 14 residues constitute the active site of iPGM. These include residues interacting with Mn^2+ ions and residues interacting with 3PGA. (B) Coordination sphere of Mn^2+ ions. The coordination sphere of both Mn^2+ ions is distorted square pyramidal. The atoms occupying the apex positions are NE2 of His462 for Mn1 and OG of Ser62 for Mn2.
Figure 5.
Figure 5 The mechanism of phosphate group transfer from 3PGA to 2PGA by B.stearothermophilus iPGM. The major intermediates in the proposed catalytic mechanism are described in the text and are depicted as follows: (A) binding of 3PGA in the active site (based on the X–ray coordinates); (B) formation of a phosphoserine intermediate; (C) repositioning of the glycerate; (D) formation of 2PGA (based on the coordinates of the 2PGA–enzyme complex model); and (E) dissociation of the 2PGA–enzyme complex.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1419-1431) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19168632 D.Lu, M.E.Wörmann, X.Zhang, O.Schneewind, A.Gründling, and P.S.Freemont (2009).
Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS.
  Proc Natl Acad Sci U S A, 106, 1584-1589.
PDB codes: 2w5q 2w5r 2w5s 2w5t
19043737 J.M.Foster, S.Raverdy, M.B.Ganatra, P.A.Colussi, C.H.Taron, and C.K.Carlow (2009).
The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies.
  Parasitol Res, 104, 1047-1052.  
19274099 M.Aivaliotis, B.Macek, F.Gnad, P.Reichelt, M.Mann, and D.Oesterhelt (2009).
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life.
  PLoS ONE, 4, e4777.  
18501204 A.L.Parrill (2008).
Lysophospholipid interactions with protein targets.
  Biochim Biophys Acta, 1781, 540-546.  
18851975 J.G.Zalatan, T.D.Fenn, and D.Herschlag (2008).
Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion.
  J Mol Biol, 384, 1174-1189.
PDB code: 3dyc
17024352 A.Djikeng, S.Raverdy, J.Foster, D.Bartholomeu, Y.Zhang, N.M.El-Sayed, and C.Carlow (2007).
Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei.
  Parasitol Res, 100, 887-892.  
17468884 L.Song, Z.Xu, and X.Yu (2007).
Molecular cloning and characterization of a phosphoglycerate mutase gene from Clonorchis sinensis.
  Parasitol Res, 101, 709-714.  
17085493 M.Nukui, L.V.Mello, J.E.Littlejohn, B.Setlow, P.Setlow, K.Kim, T.Leighton, and M.J.Jedrzejas (2007).
Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species.
  Biophys J, 92, 977-988.
PDB code: 2ify
17576516 U.Johnsen, and P.Schönheit (2007).
Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea.
  Extremophiles, 11, 647-657.  
  16880558 N.K.Lokanath, and N.Kunishima (2006).
Purification, crystallization and preliminary X-ray crystallographic analysis of the archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 788-790.  
15794763 E.Saavedra, R.Encalada, E.Pineda, R.Jasso-Chávez, and R.Moreno-Sánchez (2005).
Glycolysis in Entamoeba histolytica. Biochemical characterization of recombinant glycolytic enzymes and flux control analysis.
  FEBS J, 272, 1767-1783.  
15096219 D.G.Guerra, D.Vertommen, L.A.Fothergill-Gilmore, F.R.Opperdoes, and P.A.Michels (2004).
Characterization of the cofactor-independent phosphoglycerate mutase from Leishmania mexicana mexicana. Histidines that coordinate the two metal ions in the active site show different susceptibilities to irreversible chemical modification.
  Eur J Biochem, 271, 1798-1810.  
15234973 Y.Zhang, J.M.Foster, S.Kumar, M.Fougere, and C.K.Carlow (2004).
Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes.
  J Biol Chem, 279, 37185-37190.  
12644480 M.B.Potters, B.T.Solow, K.M.Bischoff, D.E.Graham, B.H.Lower, R.Helm, and P.J.Kennelly (2003).
Phosphoprotein with phosphoglycerate mutase activity from the archaeon Sulfolobus solfataricus.
  J Bacteriol, 185, 2112-2121.  
12076796 J.van der Oost, M.A.Huynen, and C.H.Verhees (2002).
Molecular characterization of phosphoglycerate mutase in archaea.
  FEMS Microbiol Lett, 212, 111-120.  
11512153 C.L.Verlinde, V.Hannaert, C.Blonski, M.Willson, J.J.Périé, L.A.Fothergill-Gilmore, F.R.Opperdoes, M.H.Gelb, W.G.Hol, and P.A.Michels (2001).
Glycolysis as a target for the design of new anti-trypanosome drugs.
  Drug Resist Updat, 4, 50-65.  
11682175 J.F.Collet, V.Stroobant, and E.Van Schaftingen (2001).
The 2,3-bisphosphoglycerate-independent phosphoglycerate mutase from Trypanosoma brucei: metal-ion dependency and phosphoenzyme formation.
  FEMS Microbiol Lett, 204, 39-44.  
11746679 M.Y.Galperin, and M.J.Jedrzejas (2001).
Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes.
  Proteins, 45, 318-324.  
10869096 C.L.Pearson, C.A.Loshon, L.B.Pedersen, B.Setlow, and P.Setlow (2000).
Analysis of the function of a putative 2,3-diphosphoglyceric acid-dependent phosphoglycerate mutase from Bacillus subtilis.
  J Bacteriol, 182, 4121-4123.  
11106417 J.Nairn, D.Duncan, N.E.Price, S.M.Kelly, L.A.Fothergill-Gilmore, S.Uhrinova, P.N.Barlow, D.J.Rigden, and N.C.Price (2000).
Characterization of active-site mutants of Schizosaccharomyces pombe phosphoglycerate mutase. Elucidation of the roles of amino acids involved in substrate binding and catalysis.
  Eur J Biochem, 267, 7065-7074.  
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.