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Q55DL0

- DPYS_DICDI

UniProt

Q55DL0 - DPYS_DICDI

Protein

Dihydropyrimidinase

Gene

pyd2

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 65 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      Previous versions | rss
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    Functioni

    Catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino isobutyrate.1 Publication

    Catalytic activityi

    5,6-dihydrouracil + H2O = 3-ureidopropanoate.

    Cofactori

    Binds 2 zinc ions per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi66 – 661Zinc 1
    Metal bindingi68 – 681Zinc 1
    Metal bindingi158 – 1581Zinc 1; via carbamate group
    Metal bindingi158 – 1581Zinc 2; via carbamate group
    Binding sitei163 – 1631SubstrateBy similarity
    Metal bindingi191 – 1911Zinc 2
    Metal bindingi247 – 2471Zinc 2
    Metal bindingi325 – 3251Zinc 1
    Binding sitei346 – 3461Substrate; via carbonyl oxygenBy similarity

    GO - Molecular functioni

    1. dihydropyrimidinase activity Source: dictyBase
    2. zinc ion binding Source: dictyBase

    GO - Biological processi

    1. pyrimidine nucleobase catabolic process Source: dictyBase

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiM38.973.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydropyrimidinase (EC:3.5.2.2)
    Short name:
    DHP
    Short name:
    DHPase
    Alternative name(s):
    Dihydropyrimidine amidohydrolase
    Hydantoinase
    Gene namesi
    Name:pyd2
    ORF Names:DDB_G0269246
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 1, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0269246. pyd2.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 503503DihydropyrimidinasePRO_0000312734Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei158 – 1581N6-carboxylysine1 Publication

    Post-translational modificationi

    Carbamylation allows a single lysine to coordinate two zinc ions.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi44689.DDB_0191172.

    Structurei

    Secondary structure

    1
    503
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 145
    Beta strandi16 – 183
    Beta strandi23 – 253
    Beta strandi27 – 315
    Beta strandi34 – 407
    Beta strandi50 – 523
    Beta strandi57 – 604
    Beta strandi62 – 676
    Helixi82 – 9110
    Beta strandi94 – 1018
    Helixi109 – 12113
    Beta strandi125 – 1339
    Helixi139 – 15113
    Beta strandi156 – 1627
    Turni164 – 1674
    Helixi171 – 18414
    Beta strandi187 – 1915
    Helixi195 – 20713
    Helixi214 – 2196
    Helixi223 – 23917
    Beta strandi243 – 2453
    Helixi251 – 26212
    Beta strandi267 – 2693
    Helixi273 – 2775
    Helixi280 – 2845
    Helixi288 – 2925
    Helixi306 – 31510
    Helixi331 – 3344
    Helixi335 – 3373
    Helixi341 – 3433
    Turni351 – 3533
    Helixi354 – 3629
    Turni363 – 3664
    Helixi370 – 3778
    Helixi379 – 3846
    Turni388 – 3903
    Beta strandi402 – 41211
    Turni415 – 4173
    Beta strandi421 – 4233
    Turni426 – 4294
    Beta strandi431 – 44111
    Beta strandi444 – 4485
    Helixi469 – 4713
    Helixi474 – 4818
    Helixi483 – 4864

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2FTWX-ray2.05A1-503[»]
    ProteinModelPortaliQ55DL0.
    SMRiQ55DL0. Positions 7-490.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ55DL0.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0044.
    KOiK01464.
    OMAiAVDYNIF.
    PhylomeDBiQ55DL0.

    Family and domain databases

    Gene3Di2.30.40.10. 2 hits.
    InterProiIPR011778. Hydantoinase/dihydroPyrase.
    IPR011059. Metal-dep_hydrolase_composite.
    [Graphical view]
    SUPFAMiSSF51338. SSF51338. 2 hits.
    TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q55DL0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLRVDQTGTI LIKNGTVVND DRYFKSDVLV ENGIIKEISK NIEPKEGIKV    50
    VDATDKLLLP GGIDTHTHFQ LPFMGTVSVD DFDIGTQAAV AGGTTFIIDF 100
    VIPTRGQSLL EAYDQWKKWA DEKVNCDYSL HVAITWWSEQ VSREMEILVK 150
    ERGVNSFKCF MAYKNSFMVT DQEMYHIFKR CKELGAIAQV HAENGDMVFE 200
    GQKKMLEMGI TGPEGHELSR PEALEAEATN RAIVIADSVC TPVYIVHVQS 250
    IGAADVICKH RKEGVRVYGE PIAAGLGVDG SHMWNHDWRH AAAFVMGPPI 300
    RPDPRTKGVL MDYLARGDLD CVGTDNCTFC ADQKAMGKDD FTKIPNGVNG 350
    VEDRMSIVWE NGVNTGKLTW CQFVRATSSE AARIFNIYPR KGRIDVGCDG 400
    DIVIWDPNQS KTISKDTHHH AVDFNIFEGI KVTGIAVTTI VAGNIVWSDN 450
    KLSCVKGSGR FVPRPPFGPV FDGIEQRDKV RNELLRKVDR KPYEDDNTKN 500
    SSK 503
    Length:503
    Mass (Da):56,032
    Last modified:May 24, 2005 - v1
    Checksum:i8E75DBD49100C553
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti381 – 3811A → R in AAO33383. (PubMed:12626710)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF465757 mRNA. Translation: AAO33383.1.
    AAFI02000005 Genomic DNA. Translation: EAL71973.1.
    RefSeqiXP_646121.1. XM_641029.1.

    Genome annotation databases

    EnsemblProtistsiDDB0191172; DDB0191172; DDB_G0269246.
    GeneIDi8617070.
    KEGGiddi:DDB_G0269246.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF465757 mRNA. Translation: AAO33383.1 .
    AAFI02000005 Genomic DNA. Translation: EAL71973.1 .
    RefSeqi XP_646121.1. XM_641029.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2FTW X-ray 2.05 A 1-503 [» ]
    ProteinModelPortali Q55DL0.
    SMRi Q55DL0. Positions 7-490.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0191172.

    Protein family/group databases

    MEROPSi M38.973.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0191172 ; DDB0191172 ; DDB_G0269246 .
    GeneIDi 8617070.
    KEGGi ddi:DDB_G0269246.

    Organism-specific databases

    dictyBasei DDB_G0269246. pyd2.

    Phylogenomic databases

    eggNOGi COG0044.
    KOi K01464.
    OMAi AVDYNIF.
    PhylomeDBi Q55DL0.

    Miscellaneous databases

    EvolutionaryTracei Q55DL0.
    PROi Q55DL0.

    Family and domain databases

    Gene3Di 2.30.40.10. 2 hits.
    InterProi IPR011778. Hydantoinase/dihydroPyrase.
    IPR011059. Metal-dep_hydrolase_composite.
    [Graphical view ]
    SUPFAMi SSF51338. SSF51338. 2 hits.
    TIGRFAMsi TIGR02033. D-hydantoinase. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Dihydropyrimidine amidohydrolases and dihydroorotases share the same origin and several enzymatic properties."
      Gojkovic Z., Rislund L., Andersen B., Sandrini M.P., Cook P.F., Schnackerz K.D., Piskur J.
      Nucleic Acids Res. 31:1683-1692(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    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. "The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity."
      Lohkamp B., Andersen B., Piskur J., Dobritzsch D.
      J. Biol. Chem. 281:13762-13776(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH ZINC IONS, CARBAMYLATION AT LYS-158, SUBUNIT.

    Entry informationi

    Entry nameiDPYS_DICDI
    AccessioniPrimary (citable) accession number: Q55DL0
    Secondary accession number(s): Q86LT2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 4, 2007
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 65 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3