PDBsum entry 3kbm

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Isomerase PDB id
Protein chain
388 a.a. *
_CD ×2
Waters ×210
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Room temperature x-ray structure of d-xylose isomerase compl 2cd(2+) co-factors and d12-d-alpha-glucose in the cyclic fo
Structure: Xylose isomerase. Chain: a. Engineered: yes. Other_details: the protein was purchased from hampton resea
Source: Streptomyces rubiginosus. Organism_taxid: 1929. Gene: xyla
2.00Å     R-factor:   0.178     R-free:   0.211
Authors: A.Y.Kovalevsky,L.Hanson,P.Langan
Key ref: A.Y.Kovalevsky et al. (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. PubMed id: 20541506
20-Oct-09     Release date:   16-Jun-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase
388 a.a.
388 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
Bound ligand (Het Group name = GLC)
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    
Structure 18:688-699 (2010)
PubMed id: 20541506  
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
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, P.Langan.
Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

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
20541500 B.C.Bennett, and M.Yeager (2010).
The lighter side of a sweet reaction.
  Structure, 18, 657-659.  
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