PDBsum entry 1xym

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Isomerase(intramolecular oxidoreductase) PDB id
Protein chains
386 a.a. *
GLO ×2
_OH ×2
_MG ×2
Waters ×1416
* Residue conservation analysis
PDB id:
Name: Isomerase(intramolecular oxidoreductase)
Title: The role of the divalent metal ion in sugar binding, ring op isomerization by d-xylose isomerase: replacement of a catal by an amino-acid
Structure: Xylose isomerase. Chain: a, b. Engineered: yes
Source: Streptomyces olivochromogenes. Organism_taxid: 1963
Biol. unit: Tetramer (from PQS)
1.80Å     R-factor:   0.197    
Authors: K.N.Allen,A.Lavie,G.A.Petsko,D.Ringe
Key ref:
K.N.Allen et al. (1994). Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid. Biochemistry, 33, 1488-1494. PubMed id: 7906142 DOI: 10.1021/bi00172a027
07-Dec-93     Release date:   31-May-94    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P15587  (XYLA_STROL) -  Xylose isomerase
387 a.a.
387 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.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
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/bi00172a027 Biochemistry 33:1488-1494 (1994)
PubMed id: 7906142  
Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid.
K.N.Allen, A.Lavie, A.Glasfeld, T.N.Tanada, D.P.Gerrity, S.C.Carlson, G.K.Farber, G.A.Petsko, D.Ringe.
The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron activation analysis to be 2 mol of magnesium per mole of enzyme. A plot of Mg2+ added versus Mg2+ bound to enzyme is consistent with apparent KD values of < or = 0.5-1.0 mM for one Mg2+ and < or = 2-5 mM for the second. A site-directed mutant of D-xylose isomerase was designed to remove the tighter, tetracoordinated magnesium binding site (site 1, Mg-1); Glu180 was replaced with Lys180. The stoichiometry of metal binding to this mutant, E180K, is 1 mol of magnesium per mole of enzyme. Ring-opening assays with 1-thioglucose (H2S released upon ring opening) show E180K catalyzes the opening of the sugar ring at 20% the rate of the wild-type, but E180K does not catalyze isomerization of glucose to fructose. Thus, the magnesium bound to Glu180 is essential for isomerization but not essential for ring opening. The X-ray crystallographic structures of E180K in the absence of magnesium and in the presence and absence of 250 mM glucose were obtained to 1.8-A resolution and refined to R factors of 17.7% and 19.7%, respectively. The wild-type and both E180K structures show no significant structural differences, except the epsilon-amino group of Lys180, which occupies the position usually occupied by the Mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058398 C.Roux, F.Bhatt, J.Foret, Courcy, N.Gresh, J.P.Piquemal, C.J.Jeffery, and L.Salmon (2011).
The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies.
  Proteins, 79, 203-220.  
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
18627129 D.Liu, J.Momb, P.W.Thomas, A.Moulin, G.A.Petsko, W.Fast, and D.Ringe (2008).
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.
  Biochemistry, 47, 7706-7714.
PDB codes: 3dha 3dhb 3dhc
18421591 K.Rao, S.Chelikani, P.Relue, and S.Varanasi (2008).
A novel technique that enables efficient conduct of simultaneous isomerization and fermentation (SIF) of xylose.
  Appl Biochem Biotechnol, 146, 101-117.  
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.  
15274916 H.Nishimasu, S.Fushinobu, H.Shoun, and T.Wakagi (2004).
The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea.
  Structure, 12, 949-959.
PDB code: 1umg
15240315 J.H.Park, and C.A.Batt (2004).
Restoration of a defective Lactococcus lactis xylose isomerase.
  Appl Environ Microbiol, 70, 4318-4325.  
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.  
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.  
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.  
11330684 J.Hirose, K.Maeda, H.Yokoi, and Y.Takasaki (2001).
Purification and characterization of mannose isomerase from Agrobacterium radiobacter M-1.
  Biosci Biotechnol Biochem, 65, 658-661.  
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.  
10653639 C.J.Jeffery, B.J.Bahnson, W.Chien, D.Ringe, and G.A.Petsko (2000).
Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator.
  Biochemistry, 39, 955-964.
PDB code: 1dqr
10074338 B.diSioudi, J.K.Grimsley, K.Lai, and J.R.Wild (1999).
Modification of near active site residues in organophosphorus hydrolase reduces metal stoichiometry and alters substrate specificity.
  Biochemistry, 38, 2866-2872.  
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
9844002 L.Sun, J.vanderSpek, and J.R.Murphy (1998).
Isolation and characterization of iron-independent positive dominant mutants of the diphtheria toxin repressor DtxR.
  Proc Natl Acad Sci U S A, 95, 14985-14990.  
9408951 L.M.Watkins, J.M.Kuo, M.Chen-Goodspeed, and F.M.Raushel (1997).
A combinatorial library for the binuclear metal center of bacterial phosphotriesterase.
  Proteins, 29, 553-561.  
  8801434 S.H.Bhosale, M.B.Rao, and V.V.Deshpande (1996).
Molecular and industrial aspects of glucose isomerase.
  Microbiol Rev, 60, 280-300.  
7735837 X.Wu, B.Knudsen, S.M.Feller, J.Zheng, A.Sali, D.Cowburn, H.Hanafusa, and J.Kuriyan (1995).
Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.
  Structure, 3, 215-226.
PDB codes: 1cka 1ckb
  7849593 M.R.Witmer, D.Palmieri-Young, and J.J.Villafranca (1994).
Probing the catalytic roles of n2-site glutamate residues in Escherichia coli glutamine synthetase by mutagenesis.
  Protein Sci, 3, 1746-1759.  
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.