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Protein

Uridine 5'-monophosphate synthase

Gene

pyr56

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
Orotidine 5'-phosphate = UMP + CO2.

Pathway: UMP biosynthesis via de novo pathway

This protein is involved in step 1 and 2 of the subpathway that synthesizes UMP from orotate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Uridine 5'-monophosphate synthase (pyr56)
  2. Uridine 5'-monophosphate synthase (pyr56)
This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes UMP from orotate, the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei313 – 3131By similarity

GO - Molecular functioni

  • orotate phosphoribosyltransferase activity Source: dictyBase
  • orotidine-5'-phosphate decarboxylase activity Source: dictyBase

GO - Biological processi

  • 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
  • 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
  • pyrimidine nucleobase biosynthetic process Source: dictyBase

Keywords - Molecular functioni

Decarboxylase, Glycosyltransferase, Lyase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

ReactomeiREACT_276186. Pyrimidine biosynthesis.
UniPathwayiUPA00070; UER00119.
UPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridine 5'-monophosphate synthase
Short name:
UMP synthase
Including the following 2 domains:
Orotate phosphoribosyltransferase (EC:2.4.2.10)
Short name:
OPRTase
Orotidine 5'-phosphate decarboxylase (EC:4.1.1.23)
Alternative name(s):
OMPdecase
Gene namesi
Name:pyr56
Synonyms:pyr5-6
ORF Names:DDB_G0280041
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 3, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0280041. pyr56.

Subcellular locationi

GO - Cellular componenti

  • phagocytic vesicle Source: dictyBase

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 478478Uridine 5'-monophosphate synthasePRO_0000139651Add
BLAST

Proteomic databases

PRIDEiP09556.

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB0214958.

Structurei

3D structure databases

ProteinModelPortaliP09556.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 210210OPRTaseAdd
BLAST
Regioni117 – 1259Phosphoribosyl pyrophosphate binding siteSequence Analysis
Regioni211 – 22919Domain linkerSequence AnalysisAdd
BLAST
Regioni230 – 478249OMPdecaseAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the purine/pyrimidine phosphoribosyltransferase family.Curated
In the C-terminal section; belongs to the OMP decarboxylase family.Curated

Phylogenomic databases

eggNOGiCOG0284.
InParanoidiP09556.
KOiK13421.
OMAiSMKPEFL.
PhylomeDBiP09556.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.2020. 1 hit.
HAMAPiMF_01208. PyrE.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR023031. OPRT.
IPR004467. Or_phspho_trans_dom.
IPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
PF00156. Pribosyltran. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
SSF53271. SSF53271. 1 hit.
TIGRFAMsiTIGR00336. pyrE. 1 hit.
TIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
PS00103. PUR_PYR_PR_TRANSFER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P09556-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIKELVLKL NEIDAIKLGE FKLKSGIISP IYIDLRVTVS SPPLLAAIAE
60 70 80 90 100
MMYQKVYKSG NAQETPALVC GVPYTALPIA TGMSIANNIP MVVRRKEAKA
110 120 130 140 150
YGTKQLIEGR FKEGDNVLVV EDLVTSGASV LETVRDLNSV GLKVTDVVVL
160 170 180 190 200
LDRQQGARQA LEKQGYRLHS VFTMEELINT LIEAGKLTGR TLELVQSFLD
210 220 230 240 250
ANRNVVVPLP PTLAPPAPAP IVINKPFEER AKLASNPMAS KLFTLMSSKK
260 270 280 290 300
TNLAVAADLT DKQQLLDLAE SIGSEICVLK THVDIIDNYD EEFIKSLKCI
310 320 330 340 350
AAKHNFLIFE DRKFADIGNT VKYQFENGVY KISKWADMVT VHGVAGSSIV
360 370 380 390 400
DGFKSGLKEY GSGLLLLAQM SSKGSLCVGD YTTQMIEMAN NNKEEVMGLI
410 420 430 440 450
CQERLPSMTD GLVLMTPGVQ FNSTGDAMGQ QYNTPEYIIK EKNTDVIIVG
460 470
RGIYQSNDPK SVANKYRTAA WETYQSKF
Length:478
Mass (Da):52,519
Last modified:December 4, 2007 - v2
Checksum:i0A5F45A4B0738636
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti11 – 144NEID → MKLM in CAA30443 (PubMed:2835631).Curated
Sequence conflicti155 – 1551Q → E in CAA30443 (PubMed:2835631).Curated
Sequence conflicti337 – 3371D → V in CAA30443 (PubMed:2835631).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07560 Genomic DNA. Translation: CAA30443.1.
AAFI02000035 Genomic DNA. Translation: EAL67247.1.
PIRiS03826.
RefSeqiXP_641269.1. XM_636177.1.

Genome annotation databases

EnsemblProtistsiDDB0214958; DDB0214958; DDB_G0280041.
GeneIDi8622401.
KEGGiddi:DDB_G0280041.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07560 Genomic DNA. Translation: CAA30443.1.
AAFI02000035 Genomic DNA. Translation: EAL67247.1.
PIRiS03826.
RefSeqiXP_641269.1. XM_636177.1.

3D structure databases

ProteinModelPortaliP09556.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0214958.

Proteomic databases

PRIDEiP09556.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0214958; DDB0214958; DDB_G0280041.
GeneIDi8622401.
KEGGiddi:DDB_G0280041.

Organism-specific databases

dictyBaseiDDB_G0280041. pyr56.

Phylogenomic databases

eggNOGiCOG0284.
InParanoidiP09556.
KOiK13421.
OMAiSMKPEFL.
PhylomeDBiP09556.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00119.
UPA00070; UER00120.
ReactomeiREACT_276186. Pyrimidine biosynthesis.

Miscellaneous databases

PROiP09556.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.2020. 1 hit.
HAMAPiMF_01208. PyrE.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR023031. OPRT.
IPR004467. Or_phspho_trans_dom.
IPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
PF00156. Pribosyltran. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
SSF53271. SSF53271. 1 hit.
TIGRFAMsiTIGR00336. pyrE. 1 hit.
TIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
PS00103. PUR_PYR_PR_TRANSFER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Sequence analysis of the DdPYR5-6 gene coding for UMP synthase in Dictyostelium discoideum and comparison with orotate phosphoribosyl transferases and OMP decarboxylases."
    Jacquet M., Guilbaud R., Garreau H.
    Mol. Gen. Genet. 211:441-445(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: AX3.
  2. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  3. "Proteomics fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake."
    Gotthardt D., Blancheteau V., Bosserhoff A., Ruppert T., Delorenzi M., Soldati T.
    Mol. Cell. Proteomics 5:2228-2243(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: AX2.

Entry informationi

Entry nameiUMPS_DICDI
AccessioniPrimary (citable) accession number: P09556
Secondary accession number(s): Q54VT6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: December 4, 2007
Last modified: June 24, 2015
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.