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PDBsum entry 1did

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protein ligands metals Protein-protein interface(s) links
Isomerase(intramolecular oxidoreductase) PDB id
1did
Jmol
Contents
Protein chains
393 a.a. *
Ligands
DIG ×2
Metals
_MN ×4
Waters ×504
* Residue conservation analysis
PDB id:
1did
Name: Isomerase(intramolecular oxidoreductase)
Title: Observations of reaction intermediates and the mechanism of ketose interconversion by d-xylose isomerase
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:   0.149    
Authors: C.A.Collyer,J.D.Goldberg,D.M.Blow
Key ref: C.A.Collyer and D.M.Blow (1990). Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase. Proc Natl Acad Sci U S A, 87, 1362-1366. PubMed id: 2304904 DOI: 10.1073/pnas.87.4.1362
Date:
04-Jun-92     Release date:   15-Jul-93    
PROCHECK
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 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
Bound ligand (Het Group name = DIG)
matches with 61.54% 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: 10.1073/pnas.87.4.1362 Proc Natl Acad Sci U S A 87:1362-1366 (1990)
PubMed id: 2304904  
 
 
Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase.
C.A.Collyer, D.M.Blow.
 
  ABSTRACT  
 
Crystallographic studies of D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) incubated to equilibrium with substrate/product mixtures of xylose and xylulose show electron density for a bound intermediate. The accumulation of this bound intermediate shows that the mechanism is a non-Michaelis type. Carrell et al. [Carrell, H. L., Glusker, J. P., Burger, V., Manfre, F., Tritsch, and the present authors studied crystals of the enzyme-substrate complex under different conditions and made different interpretations of the substrate density, leading to different conclusions about the enzyme mechanism. All authors agree that the bound intermediate of the sugar is in an open-chain form. It is suggested that the higher-temperature study of Carrell et al. may have produced an equilibrium of multiple states, whose density fits poorly to the open-chain substrate, and led to incorrect interpretation. The two groups also bound different closed-ring sugar analogues to the enzyme, but these analogues bind differently. A possible explanation consistent with all the data is that the enzyme operates by a hydride shift mechanism.
 

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
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
20308577 M.Moliner, Y.Román-Leshkov, and M.E.Davis (2010).
Tin-containing zeolites are highly active catalysts for the isomerization of glucose in water.
  Proc Natl Acad Sci U S A, 107, 6164-6168.  
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
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
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.  
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
11434371 A.Burger, D.Tritsch, and J.F.Biellmann (2001).
Di-tert-butyl diethylphosphoramidite as the phosphitylating reagent in the preparation of 3-deoxy-3-C-methylene-D-ribo-hexose-6-phosphate and 3-deoxy-3-C-methylene-D-erythro-pentose-5-phosphate.
  Carbohydr Res, 332, 141-149.  
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.  
  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
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
8901863 B.L.Stoddard (1996).
Caught in a chemical trap.
  Nat Struct Biol, 3, 907-909.  
  8801434 S.H.Bhosale, M.B.Rao, and V.V.Deshpande (1996).
Molecular and industrial aspects of glucose isomerase.
  Microbiol Rev, 60, 280-300.  
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.  
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
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.