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PDBsum entry 3cqi

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
3cqi
Jmol
Contents
Protein chains
277 a.a. *
Ligands
SO4 ×4
Waters ×186
* Residue conservation analysis
PDB id:
3cqi
Name: Isomerase
Title: Crystal structure of l-xylulose-5-phosphate 3-epimerase ulae complex with sulfate
Structure: L-ribulose-5-phosphate 3-epimerase ulae. Chain: a, b. Synonym: l-xylulose-5- phosphate 3-epimerase, l-ascorbate u protein e. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: o157:h7 edl933. Gene: ulae. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.187     R-free:   0.223
Authors: R.Shi,A.Matte,M.Cygler,Montreal-Kingston Bacterial Structura Genomics Initiative (Bsgi)
Key ref: R.Shi et al. (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. PubMed id: 18849419
Date:
03-Apr-08     Release date:   25-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8XDI5  (ULAE_ECO57) -  L-ribulose-5-phosphate 3-epimerase UlaE
Seq:
Struc:
284 a.a.
277 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.1.3.22  - L-ribulose-5-phosphate 3-epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-ribulose 5-phosphate = L-xylulose 5-phosphate
L-ribulose 5-phosphate
= L-xylulose 5-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     isomerase activity     3 terms  

 

 
    Added reference    
 
 
J Bacteriol 190:8137-8144 (2008)
PubMed id: 18849419  
 
 
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.
R.Shi, M.Pineda, E.Ajamian, Q.Cui, A.Matte, M.Cygler.
 
  ABSTRACT  
 
Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a beta-keto acid decarboxylation reaction to produce L-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (L-xylulose-5-phosphate 3-epimerase) and UlaF (L-ribulose-5-phosphate 4-epimerase), yielding D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel beta-strands. The enzyme binds Zn(2+), which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the beta1/alpha1 loop and alpha3' helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands beta7 and beta8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the L-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.