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PDBsum entry 1rxy

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1rxy
Jmol
Contents
Protein chains
250 a.a. *
Ligands
ACT
SO4
GOL ×3
Metals
__K
Waters ×418
* Residue conservation analysis
PDB id:
1rxy
Name: Transferase
Title: E. Coli uridine phosphorylase: type-b native
Structure: Uridine phosphorylase. Chain: a, b. Synonym: urdpase, upase. Engineered: yes. Other_details: this model represents a new native form of e where the 163-185 region of both monomers is ordered. The d containins a bound potassium ion, which allows the monomers more tightly together than those of the type-a native up di
Source: Escherichia coli. Organism_taxid: 562. Gene: udp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
Resolution:
1.70Å     R-factor:   0.130     R-free:   0.164
Authors: T.T.Caradoc-Davies,S.M.Cutfield,I.L.Lamont,J.F.Cutfield
Key ref:
T.T.Caradoc-Davies et al. (2004). Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium. J Mol Biol, 337, 337-354. PubMed id: 15003451 DOI: 10.1016/j.jmb.2004.01.039
Date:
18-Dec-03     Release date:   13-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12758  (UDP_ECOLI) -  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
= uracil
+
alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = GOL)
matches with 42.86% 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    
 
 
DOI no: 10.1016/j.jmb.2004.01.039 J Mol Biol 337:337-354 (2004)
PubMed id: 15003451  
 
 
Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium.
T.T.Caradoc-Davies, S.M.Cutfield, I.L.Lamont, J.F.Cutfield.
 
  ABSTRACT  
 
Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective effect ("uridine rescue") against the toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its antitumour activity. We have investigated UP-substrate interactions by determining the crystal structures of native Escherichia coli UP (two forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric structures confirm the overall structural similarity of UP to E.coli purine nucleoside phosphorylase (PNP) whereby, in the presence of substrate, each displays a closed conformation resulting from a concerted movement that closes the active site cleft. However, in contrast to PNP where helix segmentation is the major conformational change between the open and closed forms, in UP more extensive changes are observed. In particular a swinging movement of a flap region consisting of residues 224-234 seals the active site. This overall change in conformation results in compression of the active site cleft. Gln166 and Arg168, part of an inserted segment not seen in PNP, are key residues in the uracil binding pocket and together with a tightly bound water molecule are seen to be involved in the substrate specificity of UP. Enzyme activity shows a twofold dependence on potassium ion concentration. The presence of a potassium ion at the monomer/monomer interface induces some local rearrangement, which results in dimer stabilisation. The conservation of key residues and interactions with substrate in the phosphate and ribose binding pockets suggest that ribooxocarbenium ion formation during catalysis of UP may be similar to that proposed for E.coli PNP.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Positive difference electron density for substrate in UP complexes. All substrate molecules were omitted from the model used for phasing. (a) 5-Fluorouracil and ribose 1-phosphate contoured at 3s. (b) 5-Fluorouridine and phosphate at 2.5s. (c) 2'-Deoxyuridine and phosphate at 3s. (d) Thymidine and phosphate at 3s. (e) Stereo diagram showing a superposition of the substrates from (a), (c) and (d) in red, yellow and blue, respectively.
Figure 3.
Figure 3. Interactions involving 5-fluorouridine and phosphate with the UP active site. Hydrogen bonds =<3.3 Å are shown as dotted lines with distances indicated (Å). * Residues His8 and Arg48 are from the adjacent monomer. # The geometry of the interaction between Arg168 and O4 of uracil (shown as a wavy line) is unfavourable for hydrogen bond formation.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 337-354) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20057049 A.A.Lashkov, N.E.Zhukhlistova, A.H.Gabdoulkhakov, A.A.Shtil, R.G.Efremov, C.Betzel, and A.M.Mikhailov (2010).
The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 51-60.
PDB code: 3fwp
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
  18600781 X.K.Wei, Q.B.Ding, L.Zhang, Y.L.Guo, L.Ou, and C.L.Wang (2008).
Induction of nucleoside phosphorylase in Enterobacter aerogenes and enzymatic synthesis of adenine arabinoside.
  J Zhejiang Univ Sci B, 9, 520-526.  
17419725 G.Cacciapuoti, S.Gorassini, M.F.Mazzeo, R.A.Siciliano, V.Carbone, V.Zappia, and M.Porcelli (2007).
Biochemical and structural characterization of mammalian-like purine nucleoside phosphorylase from the Archaeon Pyrococcus furiosus.
  FEBS J, 274, 2482-2495.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
16131758 C.Schnick, M.A.Robien, A.M.Brzozowski, E.J.Dodson, G.N.Murshudov, L.Anderson, J.R.Luft, C.Mehlin, W.G.Hol, J.A.Brannigan, and A.J.Wilkinson (2005).
Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.
  Acta Crystallogr D Biol Crystallogr, 61, 1245-1254.
PDB codes: 1sq6 2bsx
  16511035 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, and A.M.Mikhailov (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.
PDB code: 1sj9
15983408 W.Bu, E.C.Settembre, M.H.el Kouni, and S.E.Ealick (2005).
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
  Acta Crystallogr D Biol Crystallogr, 61, 863-872.
PDB codes: 1u1c 1u1d 1u1e 1u1f 1u1g
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.