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PDBsum entry 1xih

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Isomerase(intramolecular oxidoreductase) PDB id
1xih
Jmol
Contents
Protein chain
385 a.a. *
Ligands
SOR
Metals
_MN
Waters ×375
* Residue conservation analysis
PDB id:
1xih
Name: Isomerase(intramolecular oxidoreductase)
Title: Modes of binding substrates and their analogues to the enzym isomerase
Structure: D-xylose isomerase. Chain: a. Engineered: yes
Source: Streptomyces rubiginosus. Organism_taxid: 1929
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.158    
Authors: H.L.Carrell,J.P.Glusker
Key ref:
H.L.Carrell et al. (1994). Modes of binding substrates and their analogues to the enzyme D-xylose isomerase. Acta Crystallogr D Biol Crystallogr, 50, 113-123. PubMed id: 15299449 DOI: 10.1107/S0907444993009345
Date:
07-Mar-94     Release date:   22-Jun-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase
Seq:
Struc:
388 a.a.
385 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 = SOR)
matches with 83.33% 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: 10.1107/S0907444993009345 Acta Crystallogr D Biol Crystallogr 50:113-123 (1994)
PubMed id: 15299449  
 
 
Modes of binding substrates and their analogues to the enzyme D-xylose isomerase.
H.L.Carrell, H.Hoier, J.P.Glusker.
 
  ABSTRACT  
 
Studies of binding of substrates and inhibitors of the enzyme D-xylose isomerase show, from X-ray diffraction data at 1.6-1.9 A resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (betaalpha)(8)-barrel structure. These binding sites are His54 and the metal ion (magnesium or manganese) that is held in place by Glul81, Asp245, Glu217 and Asp287. Possible catalytic groups have been identified in proposed mechanisms and their role in the binding of ligands is illustrated.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Binding of D-glucose. (a) Ball-and-stick view and (b) identification of some binding groups.
Figure 10.
Fig. 10. Binding of D-alkylation product (Carrell e/al., 1989). (a) Ball-and-stick view and (b) identification of some binding groups.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1994, 50, 113-123) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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
15240315 J.H.Park, and C.A.Batt (2004).
Restoration of a defective Lactococcus lactis xylose isomerase.
  Appl Environ Microbiol, 70, 4318-4325.  
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.  
  7773178 L.Shimoni, and J.P.Glusker (1995).
Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
  Protein Sci, 4, 65-74.  
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.