PDBsum entry 1u1f

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
(+ 0 more) 243 a.a. *
PO4 ×6
183 ×6
__K ×3
Waters ×536
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structure of e. Coli uridine phosphorylase complexed to 5-(m (benzyloxy)benzyl)acyclouridine (bbau)
Structure: Uridine phosphorylase. Chain: a, b, c, d, e, f. Synonym: urdpase. Upase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: udp, b3831. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
2.30Å     R-factor:   0.201     R-free:   0.228
Authors: W.Bu,E.C.Settembre,S.E.Ealick
Key ref:
W.Bu et al. (2005). Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines. Acta Crystallogr D Biol Crystallogr, 61, 863-872. PubMed id: 15983408 DOI: 10.1107/S0907444905007882
15-Jul-04     Release date:   05-Jul-05    
Go to PROCHECK summary

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

 Enzyme reactions 
   Enzyme class: E.C.  - Uridine phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = 183)
matches with 40.62% similarity
Bound ligand (Het Group name = PO4)
corresponds exactly
= uracil
+ alpha-D-ribose 1-phosphate
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  


DOI no: 10.1107/S0907444905007882 Acta Crystallogr D Biol Crystallogr 61:863-872 (2005)
PubMed id: 15983408  
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
W.Bu, E.C.Settembre, M.H.el Kouni, S.E.Ealick.
Uridine phosphorylase (UP) catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate and is a key enzyme in the pyrimidine-salvage pathway. Escherichia coli UP is structurally homologous to E. coli purine nucleoside phosphorylase and other members of the type I family of nucleoside phosphorylases. The structures of 5-benzylacyclouridine, 5-phenylthioacyclouridine, 5-phenylselenenylacyclouridine, 5-m-benzyloxybenzyl acyclouridine and 5-m-benzyloxybenzyl barbituric acid acyclonucleoside bound to the active site of E. coli UP have been determined, with resolutions ranging from 1.95 to 2.3 A. For all five complexes the acyclo sugar moiety binds to the active site in a conformation that mimics the ribose ring of the natural substrates. Surprisingly, the terminal hydroxyl group occupies the position of the nonessential 5'-hydroxyl substituent of the substrate rather than the 3'-hydroxyl group, which is normally required for catalytic activity. Until recently, inhibitors of UP were designed with limited structural knowledge of the active-site residues. These structures explain the basis of inhibition for this series of acyclouridine analogs and suggest possible additional avenues for future drug-design efforts. Furthermore, the studies can be extended to design inhibitors of human UP, for which no X-ray structure is available.
  Selected figure(s)  
Figure 2.
Figure 2 Structure of UP shown in ribbon representation. (a) UP monomer with [beta] -strands in blue and [alpha] -helices in green. BAU and phosphate are shown in stick representation bound at the active site. C atoms are colored green, N atoms blue, O atoms red and P atoms pink. (b) UP hexamer shown in ribbon representation with BAU (orange) and phosphate (red) shown bound at the active sites. Dimers with greater buried surface area are shown in similar colors. This figure was prepared with MOLSCRIPT (Kraulis, 1991 [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[bluearr.gif] ) and RASTER3D (Merritt & Bacon, 1997 [Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]-[bluearr.gif] ).
Figure 3.
Figure 3 Schematic representation of the UP active site with bound (a) 5-fluorouridine and phosphate, (b) BAU and phosphate or (c) BBBA. Hydrogen bonds are shown in dashed lines. The active-site hydrophobic pocket is indicated by a solid line flanked by the participating residues.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 863-872) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20364833 D.Paul, S.E.O'Leary, K.Rajashankar, W.Bu, A.Toms, E.C.Settembre, J.M.Sanders, T.P.Begley, and S.E.Ealick (2010).
Glycal formation in crystals of uridine phosphorylase.
  Biochemistry, 49, 3499-3509.
PDB codes: 3ku4 3kuk 3kvr 3kvv 3kvy
20070944 E.T.Larson, D.G.Mudeppa, J.R.Gillespie, N.Mueller, A.J.Napuli, J.A.Arif, J.Ross, T.L.Arakaki, A.Lauricella, G.Detitta, J.Luft, F.Zucker, C.L.Verlinde, E.Fan, W.C.Van Voorhis, F.S.Buckner, P.K.Rathod, W.G.Hol, and E.A.Merritt (2010).
The crystal structure and activity of a putative trypanosomal nucleoside phosphorylase reveal it to be a homodimeric uridine phosphorylase.
  J Mol Biol, 396, 1244-1259.
PDB code: 3bje
20856879 T.P.Roosild, and S.Castronovo (2010).
Active site conformational dynamics in human uridine phosphorylase 1.
  PLoS One, 5, e12741.
PDB code: 3nbq
19291308 T.P.Roosild, S.Castronovo, M.Fabbiani, and G.Pizzorno (2009).
Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy.
  BMC Struct Biol, 9, 14.
PDB codes: 3eue 3euf
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