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Q55DL0

- DPYS_DICDI

UniProt

Q55DL0 - DPYS_DICDI

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Protein

Dihydropyrimidinase

Gene
pyd2, DDB_G0269246
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 1631Substrate By similarity
Metal bindingi191 – 1911Zinc 2
Metal bindingi247 – 2471Zinc 2
Metal bindingi325 – 3251Zinc 1
Binding sitei346 – 3461Substrate; via carbonyl oxygen By 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
Complete GO annotation...

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
Complete GO annotation...

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-carboxylysine

Post-translational modificationi

Carbamylation allows a single lysine to coordinate two zinc ions.

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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti381 – 3811A → R in AAO33383. 1 Publication

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 64 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

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