PDBsum entry 1x9h

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Isomerase PDB id
Protein chains
301 a.a. *
SO4 ×5
F6R ×2
GOL ×4
Waters ×403
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of phosphoglucose/phosphomannose isomerase pyrobaculum aerophilum in complex with fructose 6-phosphate
Structure: Glucose-6-phosphate isomerase. Chain: a, b. Engineered: yes
Source: Pyrobaculum aerophilum. Organism_taxid: 13773. Gene: pae1610. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.50Å     R-factor:   0.153     R-free:   0.180
Authors: M.K.Swan,T Hansen,P.Schoenheit,C.Davies
Key ref:
M.K.Swan et al. (2004). Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from Pyrobaculum aerophilum: a subtle difference between distantly related enzymes. Biochemistry, 43, 14088-14095. PubMed id: 15518558 DOI: 10.1021/bi048608y
21-Aug-04     Release date:   07-Dec-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8ZWV0  (PGMI_PYRAE) -  Bifunctional phosphoglucose/phosphomannose isomerase
302 a.a.
301 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.  - Mannose-6-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

GDP-L-Fucose and GDP-mannose Biosynthesis
      Reaction: D-mannose 6-phosphate = D-fructose 6-phosphate
D-mannose 6-phosphate
Bound ligand (Het Group name = F6R)
corresponds exactly
= D-fructose 6-phosphate
      Cofactor: Zn(2+)
   Enzyme class 2: E.C.  - Glucose-6-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucose 6-phosphate = D-fructose 6-phosphate
D-glucose 6-phosphate
Bound ligand (Het Group name = F6R)
corresponds exactly
= D-fructose 6-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1021/bi048608y Biochemistry 43:14088-14095 (2004)
PubMed id: 15518558  
Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from Pyrobaculum aerophilum: a subtle difference between distantly related enzymes.
M.K.Swan, T.Hansen, P.Schönheit, C.Davies.
The crystal structure of a dual-specificity phosphoglucose/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum (PaPGI/PMI) has been determined in complex with glucose 6-phosphate at 1.16 A resolution and with fructose 6-phosphate at 1.5 A resolution. Subsequent modeling of mannose 6-phosphate (M6P) into the active site of the enzyme shows that the PMI activity of this enzyme may be due to the additional space imparted by a threonine. In PGIs from bacterial and eukaryotic sources, which cannot use M6P as a substrate, the equivalent residue is a glutamine. The increased space may permit rotation of the C2-C3 bond in M6P to facilitate abstraction of a proton from C2 by Glu203 and, after a further C2-C3 rotation of the resulting cis-enediolate, re-donation of a proton to C1 by the same residue. A proline residue (in place of a glycine in PGI) may also promote PMI activity by positioning the C1-O1 region of M6P. Thus, the PMI reaction in PaPGI/PMI probably uses a cis-enediol mechanism of catalysis, and this activity appears to arise from a subtle difference in the architecture of the enzyme, compared to bacterial and eukaryotic PGIs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058398 C.Roux, F.Bhatt, J.Foret, Courcy, N.Gresh, J.P.Piquemal, C.J.Jeffery, and L.Salmon (2011).
The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies.
  Proteins, 79, 203-220.  
19447949 S.J.Yeom, J.H.Ji, N.H.Kim, C.S.Park, and D.K.Oh (2009).
Substrate specificity of a mannose-6-phosphate isomerase from Bacillus subtilis and its application in the production of L-ribose.
  Appl Environ Microbiol, 75, 4705-4710.  
19564693 S.R.Sagurthi, G.Gowda, H.S.Savithri, and M.R.Murthy (2009).
Structures of mannose-6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: implications for catalytic mechanism.
  Acta Crystallogr D Biol Crystallogr, 65, 724-732.
PDB code: 2wfp
17253648 C.Roux, N.Gresh, L.E.Perera, J.P.Piquemal, and L.Salmon (2007).
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics.
  J Comput Chem, 28, 938-957.  
17559573 M.Reher, S.Gebhard, and P.Schönheit (2007).
Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), key enzymes of the respective modified Embden-Meyerhof pathways in the hyperthermophilic crenarchaeota Pyrobaculum aerophilum and Aeropyrum pernix.
  FEMS Microbiol Lett, 273, 196-205.  
16256419 B.Siebers, and P.Schönheit (2005).
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.
  Curr Opin Microbiol, 8, 695-705.  
16336264 T.Hansen, B.Schlichting, J.Grötzinger, M.K.Swan, C.Davies, and P.Schönheit (2005).
Mutagenesis of catalytically important residues of cupin type phosphoglucose isomerase from Archaeoglobus fulgidus.
  FEBS J, 272, 6266-6275.  
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.