spacer
spacer

PDBsum entry 1o98

Go to PDB code: 
protein ligands metals links
Isomerase PDB id
1o98
Jmol
Contents
Protein chain
509 a.a. *
Ligands
2PG
SO4 ×6
Metals
_MN ×2
Waters ×474
* Residue conservation analysis
PDB id:
1o98
Name: Isomerase
Title: 1.4a crystal structure of phosphoglycerate mutase from bacillus stearothermophilus complexed with 2-phosphoglycerate
Structure: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. Chain: a. Synonym: phosphoglycerate mutase. Engineered: yes
Source: Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.4Å     R-factor:   0.190     R-free:   0.198
Authors: D.J.Rigden,E.Lamani,J.E.Littlejohn,M.J.Jedrzejas
Key ref:
D.J.Rigden et al. (2003). Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J Mol Biol, 328, 909-920. PubMed id: 12729763 DOI: 10.1016/S0022-2836(03)00350-4
Date:
11-Dec-02     Release date:   01-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X519  (GPMI_GEOSE) -  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Seq:
Struc:
511 a.a.
509 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.5.4.2.12  - Phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
2-phospho-D-glycerate
Bound ligand (Het Group name = 2PG)
corresponds exactly
= 3-phospho-D-glycerate
      Cofactor: Manganese or cobalt
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: 10.1016/S0022-2836(03)00350-4 J Mol Biol 328:909-920 (2003)
PubMed id: 12729763  
 
 
Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling.
D.J.Rigden, E.Lamani, L.V.Mello, J.E.Littlejohn, M.J.Jedrzejas.
 
  ABSTRACT  
 
Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Comparison of crystal (white) and eigenvector 3 maximum projection (purple) structures showing the greater distance between the two domains in the latter. Substrate 2PGA (cyan) and the manganese ions (larger violet isolated spheres) are shown for orientation purposes. The Figure was made with PYMOL.
Figure 7.
Figure 7. Stereo view of the catalytic site of the phospho-iPGM-glycerate model. Glycerate is shown with white carbon and orange oxygen atoms. The aperture through which the substrate enters is towards the top of the structure, in this orientation, between residues Arg153 and Glu335. The Figure was made with PYMOL.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 909-920) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19154134 J.Dai, L.Finci, C.Zhang, S.Lahiri, G.Zhang, E.Peisach, K.N.Allen, and D.Dunaway-Mariano (2009).
Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis.
  Biochemistry, 48, 1984-1995.
PDB code: 3fm9
17951381 C.L.Naessan, W.Egge-Jacobsen, R.W.Heiniger, M.C.Wolfgang, F.E.Aas, A.Røhr, H.C.Winther-Larsen, and M.Koomey (2008).
Genetic and functional analyses of PptA, a phospho-form transferase targeting type IV pili in Neisseria gonorrhoeae.
  J Bacteriol, 190, 387-400.  
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
17050531 N.H.Yennawar, M.M.Islam, M.Conway, R.Wallin, and S.M.Hutson (2006).
Human mitochondrial branched chain aminotransferase isozyme: structural role of the CXXC center in catalysis.
  J Biol Chem, 281, 39660-39671.
PDB codes: 2hdk 2hg8 2hgw 2hgx 2hhf
  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.  
  16511148 H.A.Watkins, M.Yu, and E.N.Baker (2005).
Cloning, expression, purification and preliminary crystallographic data for Rv3214 (EntD), a predicted cofactor-dependent phosphoglycerate mutase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 753-755.  
15296734 A.Stark, A.Shkumatov, and R.B.Russell (2004).
Finding functional sites in structural genomics proteins.
  Structure, 12, 1405-1412.  
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.  
15175111 S.Mahato, D.De, D.Dutta, M.Kundu, S.Bhattacharya, M.T.Schiavone, and S.K.Bhattacharya (2004).
Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate.
  Microb Cell Fact, 3, 7.  
12832797 B.Poonperm, D.G.Guerra, I.W.McNae, L.A.Fothergill-Gilmore, and M.D.Walkinshaw (2003).
Expression, purification, crystallization and preliminary crystallographic analysis of Leishmania mexicana phosphoglycerate mutase.
  Acta Crystallogr D Biol Crystallogr, 59, 1313-1316.  
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.