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PDBsum entry 9xim

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protein ligands metals Protein-protein interface(s) links
Isomerase(intramolecular oxidoreductse) PDB id
9xim
Jmol
Contents
Protein chains
392 a.a. *
Ligands
XLS ×4
Metals
_MN ×8
Waters ×978
* Residue conservation analysis
PDB id:
9xim
Name: Isomerase(intramolecular oxidoreductse)
Title: Protein engineering of xylose (glucose) isomerase from actinoplanes missouriensis. 1. Crystallography and site- directed mutagenesis of metal binding sites
Structure: D-xylose isomerase. Chain: a, b, c, d. Engineered: yes
Source: Actinoplanes missouriensis. Organism_taxid: 1866
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.144    
Authors: J.Janin
Key ref:
J.Jenkins et al. (1992). Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites. Biochemistry, 31, 5449-5458. PubMed id: 1610791 DOI: 10.1021/bi00139a005
Date:
03-Apr-92     Release date:   15-Jul-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12851  (XYLA_ACTMI) -  Xylose isomerase
Seq:
Struc:
394 a.a.
392 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.5.3.1.5  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
D-xylopyranose
Bound ligand (Het Group name = XLS)
corresponds exactly
= D-xylulose
      Cofactor: Mg(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     carbohydrate metabolic process   3 terms 
  Biochemical function     isomerase activity     4 terms  

 

 
    Key reference    
 
 
DOI no: 10.1021/bi00139a005 Biochemistry 31:5449-5458 (1992)
PubMed id: 1610791  
 
 
Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites.
J.Jenkins, J.Janin, F.Rey, M.Chiadmi, H.van Tilbeurgh, I.Lasters, M.De Maeyer, D.Van Belle, S.J.Wodak, M.Lauwereys.
 
  ABSTRACT  
 
The structure and function of the xylose (glucose) isomerase from Actinoplanes missouriensis have been analyzed by X-ray crystallography and site-directed mutagenesis after cloning and overexpression in Escherichia coli. The crystal structure of wild-type enzyme has been refined to an R factor of 15.2% against diffraction data to 2.2-A resolution. The structures of a number of binary and ternary complexes involving wild-type and mutant enzymes, the divalent cations Mg2+, Co2+, or Mn2+, and either the substrate xylose or substrate analogs have also been determined and refined to comparable R factors. Two metal sites are identified. Metal site 1 is four-coordinated and tetrahedral in the absence of substrate and is six-coordinated and octahedral in its presence; the O2 and O4 atoms of linear inhibitors and substrate bind to metal 1. Metal site 2 is octahedral in all cases; its position changes by 0.7 A when it binds O1 of the substrate and by more than 1 A when it also binds O2; these bonds replace bonds to carboxylate ligands from the protein. Side chains involved in metal binding have been substituted by site-directed mutagenesis. The biochemical properties of the mutant enzymes are presented. Together with structural data, they demonstrate that the two metal ions play an essential part in binding substrates, in stabilizing their open form, and in catalyzing hydride transfer between the C1 and C2 positions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21429479 M.Bera, and A.Patra (2011).
Study of potential binding of biologically important sugars with a dinuclear cobalt(II) complex.
  Carbohydr Res, 346, 733-738.  
20541506 A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, and P.Langan (2010).
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
  Structure, 18, 688-699.
PDB codes: 3kbm 3kbn 3kbs 3kbv 3kbw 3kcl 3kco
20977999 H.Yoshida, K.Takeda, K.Izumori, and S.Kamitori (2010).
Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of pseudomonas stutzeri L-rhamnose isomerase.
  Protein Eng Des Sel, 23, 919-927.
PDB codes: 3m0h 3m0l 3m0m 3m0v 3m0x 3m0y
19101969 A.Burkhardt, E.T.Spielberg, S.Simon, H.Görls, A.Buchholz, and W.Plass (2009).
Hydrogen Bonds as Structural Directive towards Unusual Polynuclear Complexes: Synthesis, Structure, and Magnetic Properties of Copper(II) and Nickel(II) Complexes with a 2-Aminoglucose Ligand.
  Chemistry, 15, 1261-1271.  
17203501 M.A.Borgi, M.Rhimi, and S.Bejar (2007).
Involvement of alanine 103 residue in kinetic and physicochemical properties of glucose isomerases from Streptomyces species.
  Biotechnol J, 2, 254-259.  
16673077 F.Meilleur, E.H.Snell, M.J.van der Woerd, R.A.Judge, and D.A.Myles (2006).
A quasi-Laue neutron crystallographic study of D-xylose isomerase.
  Eur Biophys J, 35, 601-609.  
  16754978 H.Yoshida, P.Wayoon, G.Takada, K.Izumori, and S.Kamitori (2006).
Crystallization and preliminary X-ray diffraction studies of L-rhamnose isomerase from Pseudomonas stutzeri.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 550-552.  
15752361 K.L.Epting, C.Vieille, J.G.Zeikus, and R.M.Kelly (2005).
Influence of divalent cations on the structural thermostability and thermal inactivation kinetics of class II xylose isomerases.
  FEBS J, 272, 1454-1464.  
16235215 R.Kappl, K.Ranguelova, B.Koch, C.Duboc, and J.Hüttermann (2005).
Multi-frequency high-field EPR studies on metal-substituted xylose isomerase.
  Magn Reson Chem, 43, S65-S73.  
15322278 M.Garcia-Viloca, T.D.Poulsen, D.G.Truhlar, and J.Gao (2004).
Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction.
  Protein Sci, 13, 2341-2354.  
12874287 R.L.Tuinstra, and H.M.Miziorko (2003).
Investigation of conserved acidic residues in 3-hydroxy-3-methylglutaryl-CoA lyase: implications for human disease and for functional roles in a family of related proteins.
  J Biol Chem, 278, 37092-37098.  
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
11733026 C.Vieille, K.L.Epting, R.M.Kelly, and J.G.Zeikus (2001).
Bivalent cations and amino-acid composition contribute to the thermostability of Bacillus licheniformis xylose isomerase.
  Eur J Biochem, 268, 6291-6301.  
11454337 T.Tanase, T.Takei, M.Hidai, and S.Yano (2001).
Substrate-dependent chemoselective aldose-aldose and aldose-ketose isomerizations of carbohydrates promoted by a combination of calcium ion and monoamines.
  Carbohydr Res, 333, 303-312.  
11679745 Y.S.Kim, Y.J.Im, S.H.Rho, D.Sriprapundh, C.Vieille, S.W.Suh, J.G.Zeikus, and S.H.Eom (2001).
Crystallization and preliminary X-ray studies of Trp138Phe/Val185Thr xylose isomerases from Thermotoga neapolitana and Thermoanaerobacterium thermosulfurigenes.
  Acta Crystallogr D Biol Crystallogr, 57, 1686-1688.  
10924115 T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, and D.C.Rees (2000).
A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
  Biochemistry, 39, 9222-9231.
PDB codes: 1qq0 1qre 1qrf 1qrg 1qrl 1qrm
10666592 X.Zhu, M.Teng, L.Niu, C.Xu, and Y.Wang (2000).
Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 129-136.
PDB codes: 1clk 1qt1
10422261 N.Kulkarni, A.Shendye, and M.Rao (1999).
Molecular and biotechnological aspects of xylanases.
  FEMS Microbiol Rev, 23, 411-456.  
  9647799 J.M.Hess, V.Tchernajenko, C.Vieille, J.G.Zeikus, and R.M.Kelly (1998).
Thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in Escherichia coli.
  Appl Environ Microbiol, 64, 2357-2360.  
9141134 H.Hu, H.Liu, and Y.Shi (1997).
The reaction pathway of the isomerization of D-xylose catalyzed by the enzyme D-xylose isomerase: a theoretical study.
  Proteins, 27, 545-555.  
9188736 M.Fuxreiter, Z.Böcskei, A.Szeibert, E.Szabó, G.Dallmann, G.Naray-Szabo, and B.Asboth (1997).
Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca(2+)-inhibition and metal competence in the double mutant D254E/D256E.
  Proteins, 28, 183-193.  
8916223 H.Hu, Y.Y.Shi, and C.X.Wang (1996).
Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation.
  Proteins, 26, 157-166.  
  8801434 S.H.Bhosale, M.B.Rao, and V.V.Deshpande (1996).
Molecular and industrial aspects of glucose isomerase.
  Microbiol Rev, 60, 280-300.  
  7646024 C.Vieille, J.M.Hess, R.M.Kelly, and J.G.Zeikus (1995).
xylA cloning and sequencing and biochemical characterization of xylose isomerase from Thermotoga neapolitana.
  Appl Environ Microbiol, 61, 1867-1875.  
7629147 M.S.McQueney, and G.D.Markham (1995).
Investigation of monovalent cation activation of S-adenosylmethionine synthetase using mutagenesis and uranyl inhibition.
  J Biol Chem, 270, 18277-18284.  
8556430 P.W.Goodenough (1995).
A review of protein engineering for the food industry.
  Mol Biotechnol, 4, 151-166.  
  7853486 S.A.Jablonski, and C.D.Morrow (1995).
Mutation of the aspartic acid residues of the GDD sequence motif of poliovirus RNA-dependent RNA polymerase results in enzymes with altered metal ion requirements for activity.
  J Virol, 69, 1532-1539.  
  8007957 M.P.Draper, H.Y.Liu, A.H.Nelsbach, S.P.Mosley, and C.L.Denis (1994).
CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context.
  Mol Cell Biol, 14, 4522-4531.  
  8491171 F.K.Winkler, D.W.Banner, C.Oefner, D.Tsernoglou, R.S.Brown, S.P.Heathman, R.K.Bryan, P.D.Martin, K.Petratos, and K.S.Wilson (1993).
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.
  EMBO J, 12, 1781-1795.
PDB codes: 1rve 2rve 4rve
8378319 M.Meng, M.Bagdasarian, and J.G.Zeikus (1993).
The role of active-site aromatic and polar residues in catalysis and substrate discrimination by xylose isomerase.
  Proc Natl Acad Sci U S A, 90, 8459-8463.  
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.