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PDBsum entry 9xia

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Isomerase(intramolecular oxidoreductase) PDB id
9xia
Jmol
Contents
Protein chain
387 a.a. *
Ligands
DFR
Metals
_MN ×2
Waters ×299
* Residue conservation analysis
PDB id:
9xia
Name: Isomerase(intramolecular oxidoreductase)
Title: X-ray analysis of d-xylose isomerase at 1.9 angstroms: nativ in complex with substrate and with a mechanism-designed ina
Structure: Xylose isomerase. Chain: a. Engineered: yes
Source: Streptomyces rubiginosus. Organism_taxid: 1929
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.141    
Authors: H.L.Carrell,J.P.Glusker
Key ref: H.L.Carrell et al. (1989). X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator. Proc Natl Acad Sci U S A, 86, 4440-4444. PubMed id: 2734296 DOI: 10.1073/pnas.86.12.4440
Date:
11-Oct-90     Release date:   15-Oct-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase
Seq:
Struc:
388 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.5.3.1.5  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
D-xylopyranose
Bound ligand (Het Group name = DFR)
matches with 69.23% similarity
= D-xylulose
      Cofactor: Magnesium
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.86.12.4440 Proc Natl Acad Sci U S A 86:4440-4444 (1989)
PubMed id: 2734296  
 
 
X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.
H.L.Carrell, J.P.Glusker, V.Burger, F.Manfre, D.Tritsch, J.F.Biellmann.
 
  ABSTRACT  
 
The structures of crystalline D-xylose isomerase (D-xylose ketol-isomerase; EC 5.3.1.5) from Streptomyces rubiginosus and of its complexes with substrate and with an active-site-directed inhibitor have been determined by x-ray diffraction techniques and refined to 1.9-A resolution. This study identifies the active site, as well as two metal-binding sites. The metal ions are important in maintaining the structure of the active-site region and one of them binds C3-O and C5-O of the substrate forming a six-membered ring. This study has revealed a very close contact between histidine and C1 of a substrate, suggesting that this is the active-site base that abstracts a proton from substrate. The mechanism-based inhibitor is a substrate analog and is turned over by the enzyme to give a product that alkylates this same histidine, reinforcing our interpretation. The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an "open-chain" conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C1 or C2 of the substrate. A water molecule binds to C1O and C2O of the substrate and so may act as a proton donor or acceptor in the enolization of a ring-opened substrate.
 

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.  
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
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
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
19145241 J.M.Kallio, N.Hakulinen, J.P.Kallio, M.H.Niemi, S.Kärkkäinen, and J.Rouvinen (2009).
The contribution of polystyrene nanospheres towards the crystallization of proteins.
  PLoS ONE, 4, e4198.  
18416431 J.Jänis, S.Pasanen, J.Rouvinen, and P.Vainiotalo (2008).
Characterization of the pH-dependent dissociation of a multimeric metalloprotein Streptomyces rubiginosus xylose isomerase by ESI FT-ICR mass spectrometry.
  J Mass Spectrom, 43, 1376-1380.  
17937920 K.Paspaleva, E.Thomassen, N.S.Pannu, S.Iwai, G.F.Moolenaar, N.Goosen, and J.P.Abrahams (2007).
Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease.
  Structure, 15, 1316-1324.
PDB code: 2j6v
16724195 E.H.Snell, M.J.van der Woerd, M.Damon, R.A.Judge, D.A.Myles, and F.Meilleur (2006).
Optimizing crystal volume for neutron diffraction: D-xylose isomerase.
  Eur Biophys J, 35, 621-632.  
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.  
16817889 P.J.Linley, M.Landsberger, T.Kohchi, J.B.Cooper, and M.J.Terry (2006).
The molecular basis of heme oxygenase deficiency in the pcd1 mutant of pea.
  FEBS J, 273, 2594-2606.  
15983410 C.U.Kim, R.Kapfer, and S.M.Gruner (2005).
High-pressure cooling of protein crystals without cryoprotectants.
  Acta Crystallogr D Biol Crystallogr, 61, 881-890.  
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.  
15608376 R.A.Judge, K.Swift, and C.González (2005).
An ultraviolet fluorescence-based method for identifying and distinguishing protein crystals.
  Acta Crystallogr D Biol Crystallogr, 61, 60-66.  
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.  
15240315 J.H.Park, and C.A.Batt (2004).
Restoration of a defective Lactococcus lactis xylose isomerase.
  Appl Environ Microbiol, 70, 4318-4325.  
12756610 A.T.García-Sosa, R.L.Mancera, and P.M.Dean (2003).
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.
  J Mol Model, 9, 172-182.  
12595706 S.Banumathi, M.Dauter, and Z.Dauter (2003).
Phasing at high resolution using Ta6Br12 cluster.
  Acta Crystallogr D Biol Crystallogr, 59, 492-498.  
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
12037300 G.Evans, and G.Bricogne (2002).
Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment.
  Acta Crystallogr D Biol Crystallogr, 58, 976-991.
PDB codes: 1gw9 1gwa 1gwd 1gwg
12037325 R.Taylor (2002).
Life-science applications of the Cambridge Structural Database.
  Acta Crystallogr D Biol Crystallogr, 58, 879-888.  
11856836 Z.Dauter, M.Dauter, and E.Dodson (2002).
Jolly SAD.
  Acta Crystallogr D Biol Crystallogr, 58, 494-506.  
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.  
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
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.  
10368285 J.N.Varghese, M.Hrmova, and G.B.Fincher (1999).
Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.
  Structure, 7, 179-190.
PDB code: 1ex1
  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.  
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.  
8620879 P.Kristo, R.Saarelainen, R.Fagerström, S.Aho, and M.Korhola (1996).
Protein purification, and cloning and characterization of the cDNA and gene for xylose isomerase of barley.
  Eur J Biochem, 237, 240-246.  
  8801434 S.H.Bhosale, M.B.Rao, and V.V.Deshpande (1996).
Molecular and industrial aspects of glucose isomerase.
  Microbiol Rev, 60, 280-300.  
  8830690 S.Y.Liu, J.Wiegel, and F.C.Gherardini (1996).
Purification and cloning of a thermostable xylose (glucose) isomerase with an acidic pH optimum from Thermoanaerobacterium strain JW/SL-YS 489.
  J Bacteriol, 178, 5938-5945.  
8789192 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
  J Comput Aided Mol Des, 9, 500-512.  
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
8090707 R.Abagyan, D.Frishman, and P.Argos (1994).
Recognition of distantly related proteins through energy calculations.
  Proteins, 19, 132-140.  
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.  
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.  
  1624455 A.Belaich, H.P.Fierobe, D.Baty, B.Busetta, C.Bagnara-Tardif, C.Gaudin, and J.P.Belaich (1992).
The catalytic domain of endoglucanase A from Clostridium cellulolyticum: effects of arginine 79 and histidine 122 mutations on catalysis.
  J Bacteriol, 174, 4677-4682.  
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.  
1953294 A.Scheler, T.Rygus, R.Allmansberger, and W.Hillen (1991).
Molecular cloning, structure, promoters and regulatory elements for transcription of the Bacillus licheniformis encoded regulon for xylose utilization.
  Arch Microbiol, 155, 526-534.  
  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
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.  
1367634 W.J.Quax, N.T.Mrabet, R.G.Luiten, P.W.Schuurhuizen, P.Stanssens, and I.Lasters (1991).
Enhancing the thermostability of glucose isomerase by protein engineering.
  Biotechnology (N Y), 9, 738-742.  
2405386 C.A.Batt, A.C.Jamieson, and M.A.Vandeyar (1990).
Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase.
  Proc Natl Acad Sci U S A, 87, 618-622.  
2304904 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.
PDB codes: 1did 1die
2249698 C.Sudfeldt, A.Schäffer, J.H.Kägi, R.Bogumil, H.P.Schulz, S.Wulff, and H.Witzel (1990).
Spectroscopic studies on the metal-ion-binding sites of Co2(+)-substituted D-xylose isomerase from Streptomyces rubiginosus.
  Eur J Biochem, 193, 863-871.  
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.