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PDBsum entry 3kbm

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protein ligands metals links
Isomerase PDB id
3kbm
Jmol
Contents
Protein chain
388 a.a. *
Ligands
GLC
Metals
_CD ×2
Waters ×210
* Residue conservation analysis
PDB id:
3kbm
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
Resolution:
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
Date:
20-Oct-09     Release date:   16-Jun-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 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 = 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.
 
  ABSTRACT  
 
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.  
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.