PDBsum entry 1jdi

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Isomerase PDB id
Protein chains
(+ 0 more) 223 a.a. *
_ZN ×6
Waters ×433
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of l-ribulose-5-phosphate 4-epimerase
Structure: L-ribulose 5 phosphate 4-epimerase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: arad. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
2.40Å     R-factor:   0.208     R-free:   0.241
Authors: Y.Luo,J.Samuel,S.C.Mosimann,J.E.Lee,M.E.Tanner,N.C.J.Strynad
Key ref:
Y.Luo et al. (2001). The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. Biochemistry, 40, 14763-14771. PubMed id: 11732895 DOI: 10.1021/bi0112513
13-Jun-01     Release date:   23-Jan-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P08203  (ARAD_ECOLI) -  L-ribulose-5-phosphate 4-epimerase
231 a.a.
223 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.  - L-ribulose-5-phosphate 4-epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Reaction: L-ribulose 5-phosphate = D-xylulose 5-phosphate
L-ribulose 5-phosphate
= D-xylulose 5-phosphate
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   5 terms 
  Biochemical function     isomerase activity     4 terms  


    Added reference    
DOI no: 10.1021/bi0112513 Biochemistry 40:14763-14771 (2001)
PubMed id: 11732895  
The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization.
Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, M.E.Tanner, N.C.Strynadka.
The structure of L-ribulose-5-phosphate 4-epimerase from E. coli has been solved to 2.4 A resolution using X-ray diffraction data. The structure is homo-tetrameric and displays C(4) symmetry. Each subunit has a single domain comprised of a central beta-sheet flanked on either side by layers of alpha-helices. The active site is identified by the position of the catalytic zinc residue and is located at the interface between two adjacent subunits. A remarkable feature of the structure is that it shows a very close resemblance to that of L-fuculose-1-phosphate aldolase. This is consistent with the notion that both enzymes belong to a superfamily of epimerases/aldolases that catalyze carbon-carbon bond cleavage reactions via a metal-stabilized enolate intermediate. Detailed inspection of the epimerase structure, however, indicates that despite the close overall structural similarity to class II aldolases, the enzyme has evolved distinct active site features that promote its particular chemistry.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19604476 E.E.Chufán, M.De, B.A.Eipper, R.E.Mains, and L.M.Amzel (2009).
Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.
  Structure, 17, 965-973.
PDB codes: 3fvz 3fw0
18391471 H.Ashida, Y.Saito, C.Kojima, and A.Yokota (2008).
Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis.
  Biosci Biotechnol Biochem, 72, 959-967.  
19101471 H.Deng, S.M.Cross, R.P.McGlinchey, J.T.Hamilton, and D.O'Hagan (2008).
In vitro reconstituted biotransformation of 4-fluorothreonine from fluoride ion: application of the fluorinase.
  Chem Biol, 15, 1268-1276.  
18849419 R.Shi, M.Pineda, E.Ajamian, Q.Cui, A.Matte, and M.Cygler (2008).
Structure of L-xylulose-5-Phosphate 3-epimerase (UlaE) from the anaerobic L-ascorbate utilization pathway of Escherichia coli: identification of a novel phosphate binding motif within a TIM barrel fold.
  J Bacteriol, 190, 8137-8144.
PDB codes: 3cqh 3cqi 3cqj 3cqk
17331536 J.Blaszczyk, Y.Li, J.Gan, H.Yan, and X.Ji (2007).
Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase.
  J Mol Biol, 368, 161-169.
PDB codes: 2nm2 2nm3
17973403 T.Mukherjee, K.M.McCulloch, S.E.Ealick, and T.P.Begley (2007).
Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099.
  Biochemistry, 46, 13606-13615.
PDB code: 2z7b
17388809 Y.Wang, Y.Li, Y.Wu, and H.Yan (2007).
Mechanism of dihydroneopterin aldolase. NMR, equilibrium and transient kinetic studies of the Staphylococcus aureus and Escherichia coli enzymes.
  FEBS J, 274, 2240-2252.  
14635130 B.D.Silverman (2003).
Hydrophobic moments of tertiary protein structures.
  Proteins, 53, 880-888.  
12777382 F.Pojer, R.Kahlich, B.Kammerer, S.M.Li, and L.Heide (2003).
CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis.
  J Biol Chem, 278, 30661-30668.  
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
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.