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PDBsum entry 1xlm

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1xlm
Jmol
Contents
Protein chains
393 a.a. *
Ligands
XYL ×2
Metals
_AL ×4
Waters ×89
* Residue conservation analysis
PDB id:
1xlm
Name: Isomerase
Title: D254e, d256e mutant of d-xylose isomerase complexed with al3 xylitol
Structure: D-xylose isomerase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Arthrobacter sp. Nrrl. Organism_taxid: 1669. Strain: b3728. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.179     R-free:   0.222
Authors: T.Gerczei,Z.S.Bocskei,E.Szabo,G.Naray-Szabo,B.Asboth
Key ref: T.Gérczei et al. (1999). Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement. Int J Biol Macromol, 25, 329-336. PubMed id: 10456773
Date:
22-Jul-97     Release date:   28-Jan-98    
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
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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 = XYL)
corresponds exactly
= 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    
 
 
Int J Biol Macromol 25:329-336 (1999)
PubMed id: 10456773  
 
 
Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement.
T.Gérczei, Z.Böcskei, E.Szabó, B.Asbóth, G.Náray-Szabó.
 
  ABSTRACT  
 
The structure of the D254.256E double mutant of Arthrobacter xylose isomerase with Al3+ at both metal-binding sites was determined by the molecular replacement method at a conventional R-factor of 0.179. Binding of the two Al3+ does not alter the overall structure significantly. However, there are local rearrangements in the octahedral co-ordination sphere of the Al3+. The inhibitor molecule moves somewhat away from the active site. Furthermore, evidence was revealed for metal ion movement from site 2(1) to site 2(2) upon double mutation. Xylose isomerase requires two divalent metal cations for activation. The catalytic metal ion is translocated 1.8 A away from its initial position during the catalytic reaction. The fact that both activating and inactivating metals (including Al3+) were found exclusively at a single location in the double mutant was an indication that the consequently missing shuttle may account for the crippled catalytic efficiency.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17712827 E.Rezabal, J.M.Mercero, X.Lopez, and J.M.Ugalde (2007).
Protein side chains facilitate Mg/Al exchange in model protein binding sites.
  Chemphyschem, 8, 2119-2124.  
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