spacer
spacer

PDBsum entry 3kvv

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
3kvv
Jmol
Contents
Protein chains
(+ 0 more) 243 a.a. *
Ligands
URF ×6
SO4 ×6
R2B ×6
Waters ×698
* Residue conservation analysis
PDB id:
3kvv
Name: Transferase
Title: Trapping of an oxocarbenium ion intermediate in up crystals
Structure: Uridine phosphorylase. Chain: a, b, c, d, e, f. Synonym: urdpase, upase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: udp. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.175     R-free:   0.205
Authors: D.Paul,S.O'Leary,K.Rajashankar,W.Bu,A.Toms,E.Settembre,J.San T.P.Begley,S.E.Ealick
Key ref: D.Paul et al. (2010). Glycal formation in crystals of uridine phosphorylase. Biochemistry, 49, 3499-3509. PubMed id: 20364833
Date:
30-Nov-09     Release date:   28-Apr-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12758  (UDP_ECOLI) -  Uridine phosphorylase
Seq:
Struc:
253 a.a.
243 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.3  - Uridine phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
Uridine
+ phosphate
=
uracil
Bound ligand (Het Group name = URF)
matches with 88.00% similarity
+
alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = R2B)
matches with 64.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     UMP salvage   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
Biochemistry 49:3499-3509 (2010)
PubMed id: 20364833  
 
 
Glycal formation in crystals of uridine phosphorylase.
D.Paul, S.E.O'Leary, K.Rajashankar, W.Bu, A.Toms, E.C.Settembre, J.M.Sanders, T.P.Begley, S.E.Ealick.
 
  ABSTRACT  
 
Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20856879 T.P.Roosild, and S.Castronovo (2010).
Active site conformational dynamics in human uridine phosphorylase 1.
  PLoS One, 5, e12741.
PDB code: 3nbq
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.