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PDBsum entry 1sj9

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1sj9
Jmol
Contents
Protein chains
(+ 0 more) 250 a.a. *
Ligands
PO4 ×2
Waters ×168
* Residue conservation analysis
PDB id:
1sj9
Name: Transferase
Title: Crystal structure of the uridine phosphorylase from salmonel typhimurium at 2.5a resolution
Structure: Uridine phosphorylase. Chain: a, b, c, d, e, f. Synonym: urdpase, upase. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: udp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.221     R-free:   0.279
Authors: M.Dontsova,A.Gabdoulkhakov,E.Morgunova,M.Garber,S.Nikonov,C. S.Ealick,A.Mikhailov
Key ref:
M.V.Dontsova et al. (2005). Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline state. Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 337-340. PubMed id: 16511035 DOI: 10.1107/S1744309105007463
Date:
03-Mar-04     Release date:   08-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A1F6  (UDP_SALTY) -  Uridine phosphorylase
Seq:
Struc:
253 a.a.
250 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
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     cytoplasm   1 term 
  Biological process     UMP salvage   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S1744309105007463 Acta Crystallogr Sect F Struct Biol Cryst Commun 61:337-340 (2005)
PubMed id: 16511035  
 
 
Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline state.
M.V.Dontsova, A.G.Gabdoulkhakov, O.K.Molchan, A.A.Lashkov, M.B.Garber, A.S.Mironov, N.E.Zhukhlistova, E.Y.Morgunova, W.Voelter, C.Betzel, Y.Zhang, S.E.Ealick, A.M.Mikhailov.
 
  ABSTRACT  
 
Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C-N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5 A resolution and refined to an R factor of 22.1% and an Rfree of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh).
 
  Selected figure(s)  
 
Figure 1.
The structure of StUPh. (a) Electrostatic surface diagram with the structure of the hexamer color-coded by the secondary-structural elements. (b) A pair of twofold-related monomers forming a complete active site. One monomer is shown with a ribbon diagram color-coded by secondary-structural elements. The other monomer is shown as a backbone trace with the active-site residues and the phosphate ion shown in ball-and-stick representation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 April 1; 61(Pt 4): 337–340. Published online 2005 March 24. doi: 10.1107/S1744309105007463. Copyright [copyright] International Union of Crystallography 2005
Figure 2.
Stereoview showing the site of connection with the orthophosphate ion in the BD active dimer of StUPh. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 April 1; 61(Pt 4): 337–340. Published online 2005 March 24. doi: 10.1107/S1744309105007463. Copyright [copyright] International Union of Crystallography 2005
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2005, 61, 337-340) copyright 2005.  

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
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
  17909287 V.I.Timofeev, A.A.Lashkov, A.G.Gabdoulkhakov, B.P.Pavlyuk, G.S.Kachalova, C.Betzel, E.Y.Morgunova, N.E.Zhukhlistova, and A.M.Mikhailov (2007).
Isolation, crystallization and preliminary crystallographic analysis of Salmonella typhimurium uridine phosphorylase crystallized with 2,2'-anhydrouridine.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 852-854.  
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