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PDBsum entry 4e1v
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PDB id:
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Transferase
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Title:
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X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 5-fluorouracil at 2.15 a resolution
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Structure:
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Uridine phosphorylase. Chain: a, e, f, d, c, b, h, i, g. Synonym: upase, urdpase. Engineered: yes
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Source:
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Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: stm3968, stmd1.21, udp. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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2.15Å
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R-factor:
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0.196
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R-free:
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0.238
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Authors:
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A.A.Lashkov,S.E.Sotnichenko,I.I.Prokofev,A.G.Gabdoulkhakov, A.M.Mikhailov
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Key ref:
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A.A.Lashkov
et al.
(2012).
X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.
Acta Crystallogr D Biol Crystallogr,
68,
968-974.
PubMed id:
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Date:
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07-Mar-12
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Release date:
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06-Mar-13
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Supersedes:
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PROCHECK
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Headers
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References
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P0A1F6
(UDP_SALTY) -
Uridine phosphorylase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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Seq:
Struc:
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253 a.a.
248 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.2.4.2.3
- uridine phosphorylase.
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Reaction:
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uridine + phosphate = alpha-D-ribose 1-phosphate + uracil
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uridine
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+
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phosphate
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alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = )
matches with 42.86% similarity
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+
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uracil
Bound ligand (Het Group name = )
matches with 88.89% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Acta Crystallogr D Biol Crystallogr
68:968-974
(2012)
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PubMed id:
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X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.
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A.A.Lashkov,
S.E.Sotnichenko,
I.I.Prokofiev,
A.G.Gabdulkhakov,
I.I.Agapov,
A.A.Shtil,
C.Betzel,
A.S.Mironov,
A.M.Mikhailov.
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ABSTRACT
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Uridine phosphorylase (UPh), which is a key enzyme in the reutilization pathway
of pyrimidine nucleoside metabolism, is a validated target for the treatment of
infectious diseases and cancer. A detailed analysis of the interactions of UPh
with the therapeutic ligand 5-fluorouracil (5-FUra) is important for the
rational design of pharmacological inhibitors of these enzymes in prokaryotes
and eukaryotes. Expanding on the preliminary analysis of the spatial
organization of the active centre of UPh from the pathogenic bacterium
Salmonella typhimurium (StUPh) in complex with 5-FUra [Lashkov et al. (2009),
Acta Cryst. F65, 601-603], the X-ray structure of the StUPh-5-FUra complex was
analysed at atomic resolution and an in silico model of the complex formed by
the drug with UPh from Vibrio cholerae (VchUPh) was generated. These results
should be considered in the design of selective inhibitors of UPhs from various
species.
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