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PDBsum entry 1pmi

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protein metals links
Isomerase PDB id
1pmi
Jmol
Contents
Protein chain
440 a.a. *
Metals
_ZN
Waters ×322
* Residue conservation analysis
PDB id:
1pmi
Name: Isomerase
Title: Candida albicans phosphomannose isomerase
Structure: Phosphomannose isomerase. Chain: a. Synonym: pmi. Ec: 5.3.1.8
Source: Candida albicans. Organism_taxid: 5476
Resolution:
1.70Å     R-factor:   0.184    
Authors: A.Cleasby,T.Skarzynski,A.Wonacott,G.J.Davies,R.E.Hubbard, A.E.I.Proudfoot,T.N.C.Wells,M.A.Payton,A.R.Bernard
Key ref: A.Cleasby et al. (1996). The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution. Nat Struct Biol, 3, 470-479. PubMed id: 8612079
Date:
03-Apr-96     Release date:   01-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P34948  (MPI_CANAL) -  Mannose-6-phosphate isomerase
Seq:
Struc:
441 a.a.
440 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.8  - Mannose-6-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
GDP-L-Fucose and GDP-mannose Biosynthesis
      Reaction: D-mannose 6-phosphate = D-fructose 6-phosphate
D-mannose 6-phosphate
= D-fructose 6-phosphate
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   2 terms 
  Biological process     carbohydrate metabolic process   5 terms 
  Biochemical function     isomerase activity     4 terms  

 

 
    Added reference    
 
 
Nat Struct Biol 3:470-479 (1996)
PubMed id: 8612079  
 
 
The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
A.Cleasby, A.Wonacott, T.Skarzynski, R.E.Hubbard, G.J.Davies, A.E.Proudfoot, A.R.Bernard, M.A.Payton, T.N.Wells.
 
  ABSTRACT  
 
Phosphomannose isomerase (PMI) catalyses the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P). Absence of PMI activity in yeasts causes cell lysis and thus the enzyme is a potential target for inhibition and may be a route to antifungal drugs. The 1.7 A crystal structure of PMI from Candida albicans shows that the enzyme has three distinct domains. The active site lies in the central domain, contains a single essential zinc atom, and forms a deep, open cavity of suitable dimensions to contain M6P or F6P The central domain is flanked by a helical domain on one side and a jelly-roll like domain on the other.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058398 C.Roux, F.Bhatt, J.Foret, B.de 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.  
  20944231 H.L.Axelrod, P.Kozbial, D.McMullan, S.S.Krishna, M.D.Miller, P.Abdubek, C.Acosta, T.Astakhova, D.Carlton, J.Caruthers, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, Y.Elias, J.Feuerhelm, S.K.Grzechnik, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, A.T.Morse, K.D.Murphy, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, C.L.Rife, H.J.Tien, C.V.Trout, H.van den Bedem, D.Weekes, A.White, Q.Xu, C.Zubieta, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1347-1353.
PDB code: 3h50
  20862359 M.Elbaz, and S.Ben-Yehuda (2010).
The metabolic enzyme ManA reveals a link between cell wall integrity and chromosome morphology.
  PLoS Genet, 6, 0.  
19478949 G.Agarwal, M.Rajavel, B.Gopal, and N.Srinivasan (2009).
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold.
  PLoS One, 4, e5736.  
19339218 H.H.Freeze (2009).
Towards a therapy for phosphomannomutase 2 deficiency, the defect in CDG-Ia patients.
  Biochim Biophys Acta, 1792, 835-840.  
19862844 M.A.Haeuptle, and T.Hennet (2009).
Congenital disorders of glycosylation: an update on defects affecting the biosynthesis of dolichol-linked oligosaccharides.
  Hum Mutat, 30, 1628-1641.  
19754880 S.Leitgeb, G.D.Straganz, and B.Nidetzky (2009).
Functional characterization of an orphan cupin protein from Burkholderia xenovorans reveals a mononuclear nonheme Fe2+-dependent oxygenase that cleaves beta-diketones.
  FEBS J, 276, 5983-5997.  
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
  18259054 G.Gowda, S.R.Sagurthi, H.S.Savithri, and M.R.Murthy (2008).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the mannose 6-phosphate isomerase from Salmonella typhimurium.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 81-84.  
18296644 M.Koutmos, R.Pejchal, T.M.Bomer, R.G.Matthews, J.L.Smith, and M.L.Ludwig (2008).
Metal active site elasticity linked to activation of homocysteine in methionine synthases.
  Proc Natl Acad Sci U S A, 105, 3286-3291.
PDB codes: 3bof 3bol 3bq5 3bq6
18755683 T.Maruta, M.Yonemitsu, Y.Yabuta, M.Tamoi, T.Ishikawa, and S.Shigeoka (2008).
Arabidopsis phosphomannose isomerase 1, but not phosphomannose isomerase 2, is essential for ascorbic acid biosynthesis.
  J Biol Chem, 283, 28842-28851.  
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.  
18978934 N.Gresh, G.A.Cisneros, T.A.Darden, and J.P.Piquemal (2007).
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy.
  J Chem Theory Comput, 3, 1960-1986.  
16538615 P.J.Lyons, N.R.Mattatall, and H.S.Ro (2006).
Modeling and functional analysis of AEBP1, a transcriptional repressor.
  Proteins, 63, 1069-1083.  
16522801 X.Li, M.Guo, J.Fan, W.Tang, D.Wang, H.Ge, H.Rong, M.Teng, L.Niu, Q.Liu, and Q.Hao (2006).
Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases.
  Protein Sci, 15, 761-773.  
16077096 A.Teplyakov, G.Obmolova, J.Toedt, M.Y.Galperin, and G.L.Gilliland (2005).
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism.
  J Bacteriol, 187, 5520-5527.
PDB code: 1s4c
15898105 H.P.Shanahan, and J.M.Thornton (2005).
Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
  Biopolymers, 78, 318-328.  
15739204 J.Ko, L.F.Murga, P.André, H.Yang, M.J.Ondrechen, R.J.Williams, A.Agunwamba, and D.E.Budil (2005).
Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves.
  Proteins, 59, 183-195.  
15716432 T.Hansen, B.Schlichting, M.Felgendreher, and P.Schönheit (2005).
Cupin-type phosphoglucose isomerases (Cupin-PGIs) constitute a novel metal-dependent PGI family representing a convergent line of PGI evolution.
  J Bacteriol, 187, 1621-1631.  
14573596 H.Pang, M.Bartlam, Q.Zeng, H.Miyatake, T.Hisano, K.Miki, L.L.Wong, G.F.Gao, and Z.Rao (2004).
Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor.
  J Biol Chem, 279, 1491-1498.
PDB code: 1j1l
12796486 J.M.Berrisford, J.Akerboom, A.P.Turnbull, D.de Geus, S.E.Sedelnikova, I.Staton, C.W.McLeod, C.H.Verhees, J.van der Oost, D.W.Rice, and P.J.Baker (2003).
Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.
  J Biol Chem, 278, 33290-33297.
PDB code: 1plz
11983887 D.Arsenieva, R.Hardre, L.Salmon, and C.J.Jeffery (2002).
The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.
  Proc Natl Acad Sci U S A, 99, 5872-5877.
PDB code: 1koj
11863436 J.R.Tame, K.Namba, E.J.Dodson, and D.I.Roper (2002).
The crystal structure of HpcE, a bifunctional decarboxylase/isomerase with a multifunctional fold.
  Biochemistry, 41, 2982-2989.
PDB codes: 1gtt 1i7o
12042299 K.S.Hewitson, L.A.McNeill, M.V.Riordan, Y.M.Tian, A.N.Bullock, R.W.Welford, J.M.Elkins, N.J.Oldham, S.Bhattacharya, J.M.Gleadle, P.J.Ratcliffe, C.W.Pugh, and C.J.Schofield (2002).
Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family.
  J Biol Chem, 277, 26351-26355.  
12056897 R.Anand, P.C.Dorrestein, C.Kinsland, T.P.Begley, and S.E.Ealick (2002).
Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution.
  Biochemistry, 41, 7659-7669.
PDB codes: 1j58 1l3j
11148046 J.E.Jackman, C.R.Raetz, and C.A.Fierke (2001).
Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site.
  Biochemistry, 40, 514-523.  
11701646 J.Jaeken, and G.Matthijs (2001).
Congenital disorders of glycosylation.
  Annu Rev Genomics Hum Genet, 2, 129-151.  
11738598 J.M.Dunwell, A.Culham, C.E.Carter, C.R.Sosa-Aguirre, and P.W.Goodenough (2001).
Evolution of functional diversity in the cupin superfamily.
  Trends Biochem Sci, 26, 740-746.  
11606719 M.J.Ondrechen, J.G.Clifton, and D.Ringe (2001).
THEMATICS: a simple computational predictor of enzyme function from structure.
  Proc Natl Acad Sci U S A, 98, 12473-12478.  
11337405 N.Smirnoff, P.L.Conklin, and F.A.Loewus (2001).
BIOSYNTHESIS OF ASCORBIC ACID IN PLANTS: A Renaissance.
  Annu Rev Plant Physiol Plant Mol Biol, 52, 437-467.  
11165500 P.M.Clissold, and C.P.Ponting (2001).
JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta.
  Trends Biochem Sci, 26, 7-9.  
9739095 A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, B.Badet, and I.Polikarpov (1998).
Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain.
  Structure, 6, 1047-1055.
PDB code: 1moq
  10082367 I.L.Alberts, K.Nadassy, and S.J.Wodak (1998).
Analysis of zinc binding sites in protein crystal structures.
  Protein Sci, 7, 1700-1716.  
9585601 J.Jaeken, G.Matthijs, J.M.Saudubray, C.Dionisi-Vici, E.Bertini, P.de Lonlay, H.Henri, H.Carchon, E.Schollen, and E.Van Schaftingen (1998).
Phosphomannose isomerase deficiency: a carbohydrate-deficient glycoprotein syndrome with hepatic-intestinal presentation.
  Am J Hum Genet, 62, 1535-1539.  
9525984 R.Niehues, M.Hasilik, G.Alton, C.Körner, M.Schiebe-Sukumar, H.G.Koch, K.P.Zimmer, R.Wu, E.Harms, K.Reiter, K.von Figura, H.H.Freeze, H.K.Harms, and T.Marquardt (1998).
Carbohydrate-deficient glycoprotein syndrome type Ib. Phosphomannose isomerase deficiency and mannose therapy.
  J Clin Invest, 101, 1414-1420.  
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.