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PDBsum entry 1xyb

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Isomerase(intramolecular oxidoreductase) PDB id
1xyb
Jmol
Contents
Protein chains
386 a.a. *
Ligands
GLO ×2
Metals
_MG ×4
Waters ×481
* Residue conservation analysis
PDB id:
1xyb
Name: Isomerase(intramolecular oxidoreductase)
Title: X-ray crystallographic structures of d-xylose isomerase-subs complexes position the substrate and provide evidence for m movement during catalysis
Structure: Xylose isomerase. Chain: a, b. Engineered: yes
Source: Streptomyces olivochromogenes. Organism_taxid: 1963
Biol. unit: Tetramer (from PQS)
Resolution:
1.96Å     R-factor:   0.166    
Authors: A.Lavie,K.N.Allen,G.A.Petsko,D.Ringe
Key ref:
A.Lavie et al. (1994). X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. Biochemistry, 33, 5469-5480. PubMed id: 8180169 DOI: 10.1021/bi00184a016
Date:
03-Jan-94     Release date:   31-May-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15587  (XYLA_STROL) -  Xylose isomerase
Seq:
Struc:
387 a.a.
386 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = GLO)
matches with 83.33% similarity
= 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/bi00184a016 Biochemistry 33:5469-5480 (1994)
PubMed id: 8180169  
 
 
X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis.
A.Lavie, K.N.Allen, G.A.Petsko, D.Ringe.
 
  ABSTRACT  
 
The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylglucose are observed in their linear extended forms and make identical interactions with the enzyme by forming ligands to Mg-1 through O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182 through O1. Mg-2 has a water ligand that is interpreted in the crystal structure in the absence of substrate as a hydroxide ion and in the presence of substrate as a water molecule. This hydroxide ion may act as a base to deprotonate the glucose O2 and subsequently protonate the product fructose O1 concomitant with hydride transfer. Calculations of the solvent-accessible surface of possible dimers, with and without the alpha-helical C-terminal domain, suggest that the tetramer is the active form of this xylose isomerase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481775 T.D.Fenn, M.J.Schnieders, M.Mustyakimov, C.Wu, P.Langan, V.S.Pande, and A.T.Brunger (2011).
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
  Structure, 19, 523-533.
PDB code: 3qba
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
20088877 H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, and S.Kamitori (2010).
Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures.
  FEBS J, 277, 1045-1057.
PDB codes: 3itl 3ito 3itt 3itv 3itx 3ity 3iud 3iuh 3iui
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.  
19199636 J.J.Ruiz-Pernía, M.Garcia-Viloca, S.Bhattacharyya, J.Gao, D.G.Truhlar, and I.Tuñón (2009).
Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.
  J Am Chem Soc, 131, 2687-2698.  
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.  
17083959 X.Ding, B.F.Rasmussen, G.A.Petsko, and D.Ringe (2006).
Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics.
  Bioorg Chem, 34, 410-423.  
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.  
14747699 B.L.Hanson, P.Langan, A.K.Katz, X.Li, J.M.Harp, J.P.Glusker, B.P.Schoenborn, and G.J.Bunick (2004).
A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase.
  Acta Crystallogr D Biol Crystallogr, 60, 241-249.  
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.  
15190054 M.J.Maté, and C.Kleanthous (2004).
Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases.
  J Biol Chem, 279, 34763-34769.
PDB codes: 1v13 1v14 1v15
12497598 M.Garcia-Viloca, C.Alhambra, D.G.Truhlar, and J.Gao (2003).
Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.
  J Comput Chem, 24, 177-190.  
14622003 M.Garcia-Viloca, D.G.Truhlar, and J.Gao (2003).
Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase.
  Biochemistry, 42, 13558-13575.  
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
11972016 J.Gao, and D.G.Truhlar (2002).
Quantum mechanical methods for enzyme kinetics.
  Annu Rev Phys Chem, 53, 467-505.  
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.  
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.  
11440117 T.Kaneko, K.Saito, Y.Kawamura, and S.Takahashi (2001).
Molecular cloning of acid-stable glucose isomerase gene from Streptomyces olivaceoviridis E-86 by a simple two-step PCR method, and its expression in Escherichia coli.
  Biosci Biotechnol Biochem, 65, 1054-1062.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10879462 T.Kaneko, S.Takahashi, and K.Saito (2000).
Characterization of acid-stable glucose isomerase from Streptomyces sp., and development of single-step processes for high-fructose corn sweetener (HFCS) production.
  Biosci Biotechnol Biochem, 64, 940-947.  
  10091662 A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, and B.Badet (1999).
The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.
  Protein Sci, 8, 596-602.
PDB codes: 1mor 1mos
10089429 C.Chang, H.K.Song, B.C.Park, D.S.Lee, and S.W.Suh (1999).
A thermostable xylose isomerase from Thermus caldophilus: biochemical characterization, crystallization and preliminary X-ray analysis.
  Acta Crystallogr D Biol Crystallogr, 55, 294-296.  
10318897 Y.J.Sun, C.C.Chou, W.S.Chen, R.T.Wu, M.Meng, and C.D.Hsiao (1999).
The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin.
  Proc Natl Acad Sci U S A, 96, 5412-5417.
PDB code: 2pgi
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
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.  
9218783 V.Biou, R.Dumas, C.Cohen-Addad, R.Douce, D.Job, and E.Pebay-Peyroula (1997).
The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution.
  EMBO J, 16, 3405-3415.
PDB code: 1yve
8612079 A.Cleasby, A.Wonacott, T.Skarzynski, R.E.Hubbard, G.J.Davies, A.E.Proudfoot, A.R.Bernard, M.A.Payton, and T.N.Wells (1996).
The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
  Nat Struct Biol, 3, 470-479.
PDB code: 1pmi
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.  
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.