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PDBsum entry 1xll

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Isomerase(intramolecular oxidoreductase) PDB id
1xll
Jmol
Contents
Protein chains
393 a.a. *
Metals
_ZN ×4
Waters ×525
* Residue conservation analysis
PDB id:
1xll
Name: Isomerase(intramolecular oxidoreductase)
Title: Mechanism for aldose-ketose interconversion by d-xylose isom involving ring opening followed by a 1,2-hydride shift
Structure: D-xylose isomerase. Chain: a, b. Engineered: yes
Source: Arthrobacter sp.. Organism_taxid: 1669. Strain: nrrl b3728
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.164    
Authors: C.A.Collyer,K.Henrick,D.M.Blow
Key ref: C.A.Collyer et al. (1990). Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift. J Mol Biol, 212, 211-235. PubMed id: 2319597 DOI: 10.1016/0022-2836(90)90316-E
Date:
09-Oct-91     Release date:   15-Jul-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12070  (XYLA_ARTS7) -  Xylose isomerase
Seq:
Struc:
395 a.a.
393 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
= 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: 10.1016/0022-2836(90)90316-E J Mol Biol 212:211-235 (1990)
PubMed id: 2319597  
 
 
Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift.
C.A.Collyer, K.Henrick, D.M.Blow.
 
  ABSTRACT  
 
The active site and mechanism of D-xylose isomerase have been probed by determination of the crystal structures of the enzyme bound to various substrates, inhibitors and cations. Ring-opening is an obligatory first step of the reaction and is believed to be the rate-determining step for the aldose to ketose conversion. The structure of a complex with a cyclic thio-glucose has been determined and it is concluded that this is an analogue of the Michaelis complex. At -10 degrees C substrates in crystals are observed in the extended chain form. The absence of an appropriately situated base for either the cyclic or extended chain forms from the substrate binding site indicates that the isomerisation does not take place by an enediol or enediolate mechanism. Binding of a trivalent cation places an additional charge at the active site, producing a substrate complex that is analogous to a possible transition state. Of the two binding sites for divalent cations, [1] is permanently occupied under catalytic conditions and is co-ordinated to four carboxylate groups. In the absence of substrate it is exposed to solvent, and in the Michaelis complex analogue, site [1] is octahedrally coordinated, with ligands to O-3 and O-4 of the thiopyranose. In the complex with an open-chain substrate it remains octahedrally co-ordinated, with ligands to O-2 and O-4. Binding at a second cation site [2] is also necessary for catalysis and this site is believed to bind Co2+ more strongly than site [1]. This site is octahedrally co-ordinated to three carboxylate groups (bidentate co-ordination to one of them), an imidazole and a solvent molecule. It is proposed that during the hydride shift the C-O-1 and C-O-2 bonds of the substrate are polarized by the close approach of the site [2] cation. In the transition-state analogue this cation is observed at a site [2'], 1.0 A from site [2] and about 2.7 A from O-1 and O-2 of the substrate. It is likely that co-ordination of the cation to O-1 and O-2 would be concomitant with ionisation of the sugar hydroxyl group. The polarisation of C-O-1 and C-O-2 is assisted by the co-ordination of O-2 to cation [1] and O-1 to a lysine side-chain.(ABSTRACT TRUNCATED AT 400 WORDS)
 

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.  
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
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
18578508 A.Y.Kovalevsky, A.K.Katz, H.L.Carrell, L.Hanson, M.Mustyakimov, S.Z.Fisher, L.Coates, B.P.Schoenborn, G.J.Bunick, J.P.Glusker, and P.Langan (2008).
Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose.
  Biochemistry, 47, 7595-7597.
PDB code: 3cwh
18156470 H.Tamura, Y.Saito, H.Ashida, T.Inoue, Y.Kai, A.Yokota, and H.Matsumura (2008).
Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism.
  Protein Sci, 17, 126-135.
PDB codes: 2yrf 2yvk
18201926 K.Zhuo, Y.Wang, Y.Zhao, Q.Liu, and J.Wang (2008).
Interactions of calcium nitrate with pyranosides in water: a 13C NMR study.
  Spectrochim Acta A Mol Biomol Spectrosc, 71, 100-104.  
16707576 A.K.Katz, X.Li, H.L.Carrell, B.L.Hanson, P.Langan, L.Coates, B.P.Schoenborn, J.P.Glusker, and G.J.Bunick (2006).
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.
  Proc Natl Acad Sci U S A, 103, 8342-8347.
PDB codes: 2glk 2gub 2gve
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.  
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.  
12531907 N.L.Que-Gewirth, S.Lin, R.J.Cotter, and C.R.Raetz (2003).
An outer membrane enzyme that generates the 2-amino-2-deoxy-gluconate moiety of Rhizobium leguminosarum lipid A.
  J Biol Chem, 278, 12109-12119.  
12904291 S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, and M.Fischer (2003).
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.
  J Biol Chem, 278, 42256-42265.
PDB codes: 1pvw 1pvy
12777803 U.A.Ramagopal, M.Dauter, and Z.Dauter (2003).
SAD manganese in two crystal forms of glucose isomerase.
  Acta Crystallogr D Biol Crystallogr, 59, 868-875.
PDB code: 1oad
11784309 A.Lönn, M.Gárdonyi, W.van Zyl, B.Hahn-Hägerdal, and R.C.Otero (2002).
Cold adaptation of xylose isomerase from Thermus thermophilus through random PCR mutagenesis. Gene cloning and protein characterization.
  Eur J Biochem, 269, 157-163.  
12209774 R.K.Bandlish, J.Michael Hess, K.L.Epting, C.Vieille, and R.M.Kelly (2002).
Glucose-to-fructose conversion at high temperatures with xylose (glucose) isomerases from Streptomyces murinus and two hyperthermophilic Thermotoga species.
  Biotechnol Bioeng, 80, 185-194.  
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.  
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
  10548053 N.Nagano, E.G.Hutchinson, and J.M.Thornton (1999).
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
  Protein Sci, 8, 2072-2084.  
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
9103605 B.C.Park, S.Koh, C.Chang, S.W.Suh, D.S.Lee, and S.M.Byun (1997).
Cloning and expression of the gene for xylose isomerase from Thermus flavus AT62 in Escherichia coli.
  Appl Biochem Biotechnol, 62, 15-27.  
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.  
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
  8801434 S.H.Bhosale, M.B.Rao, and V.V.Deshpande (1996).
Molecular and industrial aspects of glucose isomerase.
  Microbiol Rev, 60, 280-300.  
7702743 A.E.Proudfoot, M.A.Payton, and T.N.Wells (1994).
Purification and characterization of fungal and mammalian phosphomannose isomerases.
  J Protein Chem, 13, 619-627.  
8389296 R.Bogumil, R.Kappl, J.Hüttermann, C.Sudfeldt, and H.Witzel (1993).
X- and Q-band EPR studies on the two Mn(2+)-substituted metal-binding sites of D-xylose isomerase.
  Eur J Biochem, 213, 1185-1192.  
18609636 S.H.Brown, C.Sjøholm, and R.M.Kelly (1993).
Purification and characterization of a highly thermostable glucose isomerase produced by the extremely thermophilic eubacterium, Thermotoga maritima.
  Biotechnol Bioeng, 41, 878-886.  
  1303743 L.N.Johnson (1992).
Time-resolved protein crystallography.
  Protein Sci, 1, 1237-1243.  
1620692 O.S.Smart, J.Akins, and D.M.Blow (1992).
Molecular mechanics simulations of a conformational rearrangement of D-xylose in the active site of D-xylose isomerase.
  Proteins, 13, 100-111.  
  2022613 K.Dekker, H.Yamagata, K.Sakaguchi, and S.Udaka (1991).
Xylose (glucose) isomerase gene from the thermophile Thermus thermophilus: cloning, sequencing, and comparison with other thermostable xylose isomerases.
  J Bacteriol, 173, 3078-3083.  
1724596 M.Ghatge, Y.Mawal, S.Gaikwad, and V.Deshpande (1991).
Immunoaffinity purification of glucose/xylose isomerase from Streptomyces.
  Appl Biochem Biotechnol, 31, 11-20.  
2023950 M.Meng, C.Lee, M.Bagdasarian, and J.G.Zeikus (1991).
Switching substrate preference of thermophilic xylose isomerase from D-xylose to D-glucose by redesigning the substrate binding pocket.
  Proc Natl Acad Sci U S A, 88, 4015-4019.  
2006134 M.Whitlow, A.J.Howard, B.C.Finzel, T.L.Poulos, E.Winborne, and G.L.Gilliland (1991).
A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose.
  Proteins, 9, 153-173.
PDB codes: 1xis 2xis 3xis 4xis
1848816 R.Bogumil, J.Hüttermann, R.Kappl, R.Stabler, C.Sudfeldt, and H.Witzel (1991).
Visible, EPR and electron nuclear double-resonance spectroscopic studies on the two metal-binding sites of oxovanadium (IV)-substituted D-xylose isomerase.
  Eur J Biochem, 196, 305-312.  
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.