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PDBsum entry 1dqr

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Isomerase PDB id
1dqr
Jmol
Contents
Protein chains
555 a.a. *
Ligands
6PG ×2
Waters ×370
* Residue conservation analysis
PDB id:
1dqr
Name: Isomerase
Title: Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator
Structure: Phosphoglucose isomerase. Chain: a, b. Ec: 5.3.1.9
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: muscle
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.212     R-free:   0.265
Authors: B.J.Bahnson,C.J.Jeffery,D.Ringe,G.A.Petsko
Key ref:
C.J.Jeffery et al. (2000). Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator. Biochemistry, 39, 955-964. PubMed id: 10653639 DOI: 10.1021/bi991604m
Date:
05-Jan-00     Release date:   09-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9N1E2  (G6PI_RABIT) -  Glucose-6-phosphate isomerase
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
555 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.9  - 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 = 6PG)
matches with 94.00% similarity
= D-fructose 6-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     angiogenesis   3 terms 
  Biochemical function     isomerase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi991604m Biochemistry 39:955-964 (2000)
PubMed id: 10653639  
 
 
Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator.
C.J.Jeffery, B.J.Bahnson, W.Chien, D.Ringe, G.A.Petsko.
 
  ABSTRACT  
 
The multifunctional protein phosphoglucose isomerase, also known as neuroleukin, autocrine motility factor, and differentiation and maturation mediator, has different roles inside and outside the cell. In the cytoplasm, it catalyzes the second step in glycolysis. Outside the cell, it serves as a nerve growth factor and cytokine. We have determined the three-dimensional structure of rabbit muscle phosphoglucose isomerase complexed with the competitive inhibitor D-gluconate 6-phosphate by X-ray crystallography at 2.5 A resolution. The structure shows that the enzyme is a dimer with two alpha/beta-sandwich domains in each subunit. The location of the bound D-gluconate 6-phosphate inhibitor leads to the identification of residues involved in substrate specificity (Ser209, Ser159, Thr214, Thr217, and Thr211). The results of previously published kinetic studies suggest that a lysine and a histidine are involved in the catalytic mechanism. The crystal structure suggests active site residues Lys518 and His388 might be these residues. In addition, the positions of amino acid residues that are substituted in the genetic disease nonspherocytic hemolytic anemia suggest how these substitutions can result in altered catalysis or protein stability.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20628759 M.A.Troncoso-Ponce, J.Rivoal, F.J.Cejudo, S.Dorion, R.Garcés, and E.Martínez-Force (2010).
Cloning, biochemical characterisation, tissue localisation and possible post-translational regulatory mechanism of the cytosolic phosphoglucose isomerase from developing sunflower seeds.
  Planta, 232, 845-859.  
19424742 B.Wang, W.B.Watt, C.Aakre, and N.Hawthorne (2009).
Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase.
  J Mol Evol, 68, 433-447.  
19531650 T.Funasaka, V.Hogan, and A.Raz (2009).
Phosphoglucose isomerase/autocrine motility factor mediates epithelial and mesenchymal phenotype conversions in breast cancer.
  Cancer Res, 69, 5349-5356.  
  19052382 Y.L.Lee, and T.T.Li (2008).
Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1181-1183.  
17828376 T.Funasaka, and A.Raz (2007).
The role of autocrine motility factor in tumor and tumor microenvironment.
  Cancer Metastasis Rev, 26, 725-735.  
16756667 D.Steinke, S.Hoegg, H.Brinkmann, and A.Meyer (2006).
Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates.
  BMC Biol, 4, 16.  
15684571 A.Haga (2005).
[Possibility that AMF will serve as a target molecule for the diagnosis and treatment of a metastatic neoplasm]
  Yakugaku Zasshi, 125, 169-175.  
15689508 J.H.Lee, and C.J.Jeffery (2005).
The crystal structure of rabbit phosphoglucose isomerase complexed with D-sorbitol-6-phosphate, an analog of the open chain form of D-glucose-6-phosphate.
  Protein Sci, 14, 727-734.
PDB code: 1xtb
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.  
15637053 T.Yanagawa, T.Funasaka, S.Tsutsumi, T.Raz, N.Tanaka, and A.Raz (2005).
Differential regulation of phosphoglucose isomerase/autocrine motility factor activities by protein kinase CK2 phosphorylation.
  J Biol Chem, 280, 10419-10426.  
15206941 A.T.Cordeiro, P.A.Michels, L.F.Delboni, and O.H.Thiemann (2004).
The crystal structure of glucose-6-phosphate isomerase from Leishmania mexicana reveals novel active site features.
  Eur J Biochem, 271, 2765-2772.
PDB codes: 1q50 1t10
15103138 A.T.Cordeiro, R.Hardré, P.A.Michels, L.Salmon, L.F.Delboni, and O.H.Thiemann (2004).
Leishmania mexicana mexicana glucose-6-phosphate isomerase: crystallization, molecular-replacement solution and inhibition.
  Acta Crystallogr D Biol Crystallogr, 60, 915-919.  
14960389 L.W.Hardy, and N.P.Peet (2004).
The multiple orthogonal tools approach to define molecular causation in the validation of druggable targets.
  Drug Discov Today, 9, 117-126.  
15252053 M.K.Swan, T.Hansen, P.Schönheit, and C.Davies (2004).
A novel phosphoglucose isomerase (PGI)/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16-A resolution.
  J Biol Chem, 279, 39838-39845.
PDB codes: 1tzb 1tzc
15502335 N.Naba, N.Tanaka, K.Shiraiwa, Y.Kusakabe, T.Funasaka, A.Haga, H.Nagase, A.Raz, and K.T.Nakamura (2004).
Crystallization and preliminary X-ray crystallographic studies of mouse autocrine motility factor.
  Acta Crystallogr D Biol Crystallogr, 60, 2084-2086.  
14551194 T.Hansen, D.Wendorff, and P.Schönheit (2004).
Bifunctional phosphoglucose/phosphomannose isomerases from the Archaea Aeropyrum pernix and Thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.
  J Biol Chem, 279, 2262-2272.  
12595702 C.Davies, and H.Muirhead (2003).
Structure of native phosphoglucose isomerase from rabbit: conformational changes associated with catalytic function.
  Acta Crystallogr D Biol Crystallogr, 59, 453-465.
PDB code: 1n8t
12777791 C.Davies, H.Muirhead, and J.Chirgwin (2003).
The structure of human phosphoglucose isomerase complexed with a transition-state analogue.
  Acta Crystallogr D Biol Crystallogr, 59, 1111-1113.
PDB code: 1nuh
12888574 M.Amraei, Z.Jia, P.Reboul, and I.R.Nabi (2003).
Acid-induced conformational changes in phosphoglucose isomerase result in its increased cell surface association and deposition on fibronectin fibrils.
  J Biol Chem, 278, 38935-38941.  
12787250 M.L.Engel, A.Chaboud, C.Dumas, and S.McCormick (2003).
Sperm cells of Zea mays have a complex complement of mRNAs.
  Plant J, 34, 697-707.  
12727381 S.Chakrabarti, S.Bhattacharya, and S.K.Bhattacharya (2003).
Biochemical engineering: cues from cells.
  Trends Biotechnol, 21, 204-209.  
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
12211039 E.S.Rangarajan, J.Sivaraman, A.Matte, and M.Cygler (2002).
Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli.
  Proteins, 48, 737-740.
PDB code: 1lkz
  12038528 V.S.Ford, and L.D.Gottlieb (2002).
Single mutations silence PGiC2 genes in two very recent allotetraploid species of Clarkia.
  Evolution Int J Org Evolution, 56, 699-707.  
11264592 A.T.Cordeiro, P.H.Godoi, L.F.Delboni, G.Oliva, and O.H.Thiemann (2001).
Human phosphoglucose isomerase: expression, purification, crystallization and preliminary crystallographic analysis.
  Acta Crystallogr D Biol Crystallogr, 57, 592-595.  
11327814 C.J.Jeffery, R.Hardré, and L.Salmon (2001).
Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonate identifies the role of Glu357 in catalysis.
  Biochemistry, 40, 1560-1566.
PDB code: 1g98
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.  
11180386 H.Chen, Z.Zhao, T.M.Hallis, Z.Guo, and Liu Hw (2001).
Insights into the Branched-Chain Formation of Mycarose: Methylation Catalyzed by an (S)-Adenosylmethionine-Dependent Methyltransferase We are grateful to Dr. Eugene Seno and the Lilly Research Laboratories for their generous gift of the plasmid pHJL311 and to the National Institutes of Health for grants (GM 35 906 and 54 346). H.-w.L. also thanks the National Institute of General Medical Sciences for a MERIT Award. T.M.H. was a trainee of the National Institute of General Medical Sciences (Biotechnology Training Grant: 2 T32 GM08347).
  Angew Chem Int Ed Engl, 40, 607-610.  
11425306 J.H.Lee, K.Z.Chang, V.Patel, and C.J.Jeffery (2001).
Crystal structure of rabbit phosphoglucose isomerase complexed with its substrate D-fructose 6-phosphate.
  Biochemistry, 40, 7799-7805.
PDB code: 1hox
11344151 T.Hansen, M.Oehlmann, and P.Schönheit (2001).
Novel type of glucose-6-phosphate isomerase in the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 183, 3428-3435.  
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
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.