PDBsum entry 1xru

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Isomerase PDB id
Protein chains
281 a.a. *
1PE ×2
_ZN ×2
Waters ×457
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of 5-keto-4-deoxyuronate isomerase from es coli
Structure: 4-deoxy-l-threo-5-hexosulose-uronate ketol-isomer chain: a, b. Synonym: 5-keto-4-deoxyuronate isomerase, dki isomerase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: kdui. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
1.94Å     R-factor:   0.164     R-free:   0.191
Authors: R.L.Crowther,M.M.Georgiadis
Key ref:
R.L.Crowther and M.M.Georgiadis (2005). The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Proteins, 61, 680-684. PubMed id: 16152643 DOI: 10.1002/prot.20598
15-Oct-04     Release date:   05-Apr-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q46938  (KDUI_ECOLI) -  4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
278 a.a.
281 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 5-dehydro-4-deoxy-D-glucuronate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate
= 3-deoxy-D-glycero-2,5-hexodiulosonate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     protein binding     7 terms  


    Added reference    
DOI no: 10.1002/prot.20598 Proteins 61:680-684 (2005)
PubMed id: 16152643  
The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli.
R.L.Crowther, M.M.Georgiadis.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. General structural features of KduI. A: A ribbon rendering of a single subunit of KduI is shown with helices in crimson, strands in orange, and coils in purple. For clarity, the strands are designated by number only. 1 designates the short 3[10] helix. B: The hexamer of KduI is generated from the two subunits in the asymmetric unit by the symmetry operators (-Y, X-Y, Z) and (Y-X, -X, Z). Helices are shown as crimson cylinders. The strands and coils of the A molecules are shown in orange while the strands and coils of the B molecules are shown in blue. C: The relative locations of the metal atom and the defined PEG molecule are shown. A 1- SA-omit map of the region surrounding K165 clearly shows the extra density due to the PEG molecule. A 5 -anomalous difference map showing the putative zinc atom is also shown. A water molecule positioned midway between the metal and PEG molecule is also shown.
Figure 2.
Figure 2. Comparative sequence analysis. A PSI-BLAST alignment of selected proteins with significant sequence homology to KduI is shown.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 680-684) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19478949 G.Agarwal, M.Rajavel, B.Gopal, and N.Srinivasan (2009).
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold.
  PLoS One, 4, e5736.  
19159926 P.Richard, and S.Hilditch (2009).
D-galacturonic acid catabolism in microorganisms and its biotechnological relevance.
  Appl Microbiol Biotechnol, 82, 597-604.  
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