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P12758

- UDP_ECOLI

UniProt

P12758 - UDP_ECOLI

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Protein

Uridine phosphorylase

Gene

udp

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.

Catalytic activityi

Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.

Pathwayi

GO - Molecular functioni

  1. identical protein binding Source: EcoCyc
  2. uridine phosphorylase activity Source: EcoCyc

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: EcoliWiki
  2. nucleotide catabolic process Source: InterPro
  3. UMP salvage Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciEcoCyc:URPHOS-MONOMER.
ECOL316407:JW3808-MONOMER.
MetaCyc:URPHOS-MONOMER.
UniPathwayiUPA00574; UER00633.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridine phosphorylase (EC:2.4.2.3)
Short name:
UPase
Short name:
UrdPase
Gene namesi
Name:udp
Ordered Locus Names:b3831, JW3808
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11045. udp.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi5 – 51D → A, E or N: No change in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed3 Publications
Chaini2 – 253252Uridine phosphorylasePRO_0000063183Add
BLAST

Proteomic databases

PaxDbiP12758.
PRIDEiP12758.

2D gel databases

SWISS-2DPAGEP12758.

Expressioni

Gene expression databases

GenevestigatoriP12758.

Interactioni

Subunit structurei

Homohexamer. The homohexamer shows 4-fold, 6-fold or 8-fold symmetry.

Protein-protein interaction databases

DIPiDIP-11075N.
IntActiP12758. 4 interactions.
MINTiMINT-6478293.
STRINGi511145.b3831.

Structurei

Secondary structure

1
253
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 94Combined sources
Helixi13 – 164Combined sources
Beta strandi21 – 233Combined sources
Helixi28 – 303Combined sources
Helixi31 – 355Combined sources
Beta strandi38 – 4710Combined sources
Beta strandi50 – 578Combined sources
Beta strandi60 – 656Combined sources
Helixi71 – 8313Combined sources
Beta strandi88 – 9710Combined sources
Beta strandi107 – 11610Combined sources
Helixi119 – 1224Combined sources
Helixi134 – 14613Combined sources
Beta strandi151 – 16010Combined sources
Helixi164 – 1663Combined sources
Beta strandi171 – 1733Combined sources
Helixi178 – 1803Combined sources
Helixi183 – 1897Combined sources
Beta strandi194 – 1985Combined sources
Helixi199 – 2079Combined sources
Turni208 – 2103Combined sources
Beta strandi212 – 22211Combined sources
Turni223 – 2253Combined sources
Helixi231 – 25121Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K3FX-ray2.50A/B/C/D/E/F1-253[»]
1LX7X-ray2.00A/B1-253[»]
1RXCX-ray2.35A/B/C/D/E/F/G/H/I/J/K/L1-253[»]
1RXSX-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o1-253[»]
1RXUX-ray3.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-253[»]
1RXYX-ray1.70A/B1-253[»]
1T0UX-ray2.20A/B1-253[»]
1TGVX-ray2.20A/B1-253[»]
1TGYX-ray2.20A/B1-253[»]
1U1CX-ray2.20A/B/C/D/E/F2-253[»]
1U1DX-ray2.00A/B/C/D/E/F2-253[»]
1U1EX-ray2.00A/B/C/D/E/F2-253[»]
1U1FX-ray2.30A/B/C/D/E/F2-253[»]
1U1GX-ray1.95A/B/C/D/E/F2-253[»]
3KVVX-ray1.80A/B/C/D/E/F1-253[»]
ProteinModelPortaliP12758.
SMRiP12758. Positions 4-253.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12758.

Family & Domainsi

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.Curated

Phylogenomic databases

eggNOGiCOG2820.
HOGENOMiHOG000274897.
InParanoidiP12758.
KOiK00757.
OMAiNVMNFEM.
OrthoDBiEOG676Z3T.
PhylomeDBiP12758.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
InterProiIPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
IPR010058. Uridine_phosphorylase.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR01718. Uridine-psphlse. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P12758-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF
60 70 80 90 100
TTWRAELDGK PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP
110 120 130 140 150
HINVGDVLVT TASVRLDGAS LHFAPLEFPA VADFECTTAL VEAAKSIGAT
160 170 180 190 200
THVGVTASSD TFYPGQERYD TYSGRVVRHF KGSMEEWQAM GVMNYEMESA
210 220 230 240 250
TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH AVKIVVEAAR

RLL
Length:253
Mass (Da):27,159
Last modified:January 23, 2007 - v3
Checksum:i7446DE45BA04D88D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti11 – 111L → Y AA sequence (PubMed:8899705)Curated
Sequence conflicti15 – 151D → Y AA sequence (PubMed:8899705)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15689 Genomic DNA. Translation: CAA33724.1.
M87049 Genomic DNA. Translation: AAA67626.1.
U00096 Genomic DNA. Translation: AAC76834.1.
AP009048 Genomic DNA. Translation: BAE77470.1.
PIRiS05491.
RefSeqiNP_418275.1. NC_000913.3.
YP_491611.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76834; AAC76834; b3831.
BAE77470; BAE77470; BAE77470.
GeneIDi12934305.
948987.
KEGGiecj:Y75_p3347.
eco:b3831.
PATRICi32123163. VBIEscCol129921_3947.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15689 Genomic DNA. Translation: CAA33724.1 .
M87049 Genomic DNA. Translation: AAA67626.1 .
U00096 Genomic DNA. Translation: AAC76834.1 .
AP009048 Genomic DNA. Translation: BAE77470.1 .
PIRi S05491.
RefSeqi NP_418275.1. NC_000913.3.
YP_491611.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1K3F X-ray 2.50 A/B/C/D/E/F 1-253 [» ]
1LX7 X-ray 2.00 A/B 1-253 [» ]
1RXC X-ray 2.35 A/B/C/D/E/F/G/H/I/J/K/L 1-253 [» ]
1RXS X-ray 2.80 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o 1-253 [» ]
1RXU X-ray 3.10 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R 1-253 [» ]
1RXY X-ray 1.70 A/B 1-253 [» ]
1T0U X-ray 2.20 A/B 1-253 [» ]
1TGV X-ray 2.20 A/B 1-253 [» ]
1TGY X-ray 2.20 A/B 1-253 [» ]
1U1C X-ray 2.20 A/B/C/D/E/F 2-253 [» ]
1U1D X-ray 2.00 A/B/C/D/E/F 2-253 [» ]
1U1E X-ray 2.00 A/B/C/D/E/F 2-253 [» ]
1U1F X-ray 2.30 A/B/C/D/E/F 2-253 [» ]
1U1G X-ray 1.95 A/B/C/D/E/F 2-253 [» ]
3KVV X-ray 1.80 A/B/C/D/E/F 1-253 [» ]
ProteinModelPortali P12758.
SMRi P12758. Positions 4-253.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-11075N.
IntActi P12758. 4 interactions.
MINTi MINT-6478293.
STRINGi 511145.b3831.

2D gel databases

SWISS-2DPAGE P12758.

Proteomic databases

PaxDbi P12758.
PRIDEi P12758.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76834 ; AAC76834 ; b3831 .
BAE77470 ; BAE77470 ; BAE77470 .
GeneIDi 12934305.
948987.
KEGGi ecj:Y75_p3347.
eco:b3831.
PATRICi 32123163. VBIEscCol129921_3947.

Organism-specific databases

EchoBASEi EB1038.
EcoGenei EG11045. udp.

Phylogenomic databases

eggNOGi COG2820.
HOGENOMi HOG000274897.
InParanoidi P12758.
KOi K00757.
OMAi NVMNFEM.
OrthoDBi EOG676Z3T.
PhylomeDBi P12758.

Enzyme and pathway databases

UniPathwayi UPA00574 ; UER00633 .
BioCyci EcoCyc:URPHOS-MONOMER.
ECOL316407:JW3808-MONOMER.
MetaCyc:URPHOS-MONOMER.

Miscellaneous databases

EvolutionaryTracei P12758.
PROi P12758.

Gene expression databases

Genevestigatori P12758.

Family and domain databases

Gene3Di 3.40.50.1580. 1 hit.
InterProi IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
IPR010058. Uridine_phosphorylase.
[Graphical view ]
PANTHERi PTHR21234. PTHR21234. 1 hit.
Pfami PF01048. PNP_UDP_1. 1 hit.
[Graphical view ]
SUPFAMi SSF53167. SSF53167. 1 hit.
TIGRFAMsi TIGR01718. Uridine-psphlse. 1 hit.
PROSITEi PS01232. PNP_UDP_1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene."
    Walton L., Richards C.A., Elwell L.P.
    Nucleic Acids Res. 17:6741-6741(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
    Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
    Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases."
    Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.
    Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-18.
  6. Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.
    Submitted (FEB-1996) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-12.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. "FIS is a regulator of metabolism in Escherichia coli."
    Gonzalez-Gil G., Bringmann P., Kahmann R.
    Mol. Microbiol. 22:21-29(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-16.
    Strain: K12.
  8. "Protein engineering of uridine phosphorylase from Escherichia coli K-12. I. Cloning and expression of uridine phosphorylase genes from Klebsiella aerogenes and Salmonella typhimurium in E. coli."
    Veiko V.P., Chebotaev D.V., Ovcharova I.V., Gul'Ko L.B.
    Bioorg. Khim. 24:381-387(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-5.
  9. "Atomic structure at 2.5-A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice."
    Morgunova E.Y., Mikhailov A.M., Popov A.N., Blagova E.V., Smirnova E.A., Vainshtein B.K., Mao C., Armstrong S.H.R., Ealick S.E., Komissarov A.A., Linkova E.V., Burlakova A.A., Mironov A.S., Debabov V.G.
    FEBS Lett. 367:183-187(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  10. "Structure of Escherichia coli uridine phosphorylase at 2.0 A."
    Burling F.T., Kniewel R., Buglino J.A., Chadha T., Beckwith A., Lima C.D.
    Acta Crystallogr. D 59:73-76(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Entry informationi

Entry nameiUDP_ECOLI
AccessioniPrimary (citable) accession number: P12758
Secondary accession number(s): Q2M8D6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 149 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3