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Protein

Dihydropyrimidinase

Gene

pyd2

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: 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

Zn2+Note: Binds 2 Zn2+ 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
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-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 – 145Combined sources
Beta strandi16 – 183Combined sources
Beta strandi23 – 253Combined sources
Beta strandi27 – 315Combined sources
Beta strandi34 – 407Combined sources
Beta strandi50 – 523Combined sources
Beta strandi57 – 604Combined sources
Beta strandi62 – 676Combined sources
Helixi82 – 9110Combined sources
Beta strandi94 – 1018Combined sources
Helixi109 – 12113Combined sources
Beta strandi125 – 1339Combined sources
Helixi139 – 15113Combined sources
Beta strandi156 – 1627Combined sources
Turni164 – 1674Combined sources
Helixi171 – 18414Combined sources
Beta strandi187 – 1915Combined sources
Helixi195 – 20713Combined sources
Helixi214 – 2196Combined sources
Helixi223 – 23917Combined sources
Beta strandi243 – 2453Combined sources
Helixi251 – 26212Combined sources
Beta strandi267 – 2693Combined sources
Helixi273 – 2775Combined sources
Helixi280 – 2845Combined sources
Helixi288 – 2925Combined sources
Helixi306 – 31510Combined sources
Helixi331 – 3344Combined sources
Helixi335 – 3373Combined sources
Helixi341 – 3433Combined sources
Turni351 – 3533Combined sources
Helixi354 – 3629Combined sources
Turni363 – 3664Combined sources
Helixi370 – 3778Combined sources
Helixi379 – 3846Combined sources
Turni388 – 3903Combined sources
Beta strandi402 – 41211Combined sources
Turni415 – 4173Combined sources
Beta strandi421 – 4233Combined sources
Turni426 – 4294Combined sources
Beta strandi431 – 44111Combined sources
Beta strandi444 – 4485Combined sources
Helixi469 – 4713Combined sources
Helixi474 – 4818Combined sources
Helixi483 – 4864Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiQ55DL0.
KOiK01464.
OMAiQHQDSLW.
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

        10         20         30         40         50
MLRVDQTGTI LIKNGTVVND DRYFKSDVLV ENGIIKEISK NIEPKEGIKV
60 70 80 90 100
VDATDKLLLP GGIDTHTHFQ LPFMGTVSVD DFDIGTQAAV AGGTTFIIDF
110 120 130 140 150
VIPTRGQSLL EAYDQWKKWA DEKVNCDYSL HVAITWWSEQ VSREMEILVK
160 170 180 190 200
ERGVNSFKCF MAYKNSFMVT DQEMYHIFKR CKELGAIAQV HAENGDMVFE
210 220 230 240 250
GQKKMLEMGI TGPEGHELSR PEALEAEATN RAIVIADSVC TPVYIVHVQS
260 270 280 290 300
IGAADVICKH RKEGVRVYGE PIAAGLGVDG SHMWNHDWRH AAAFVMGPPI
310 320 330 340 350
RPDPRTKGVL MDYLARGDLD CVGTDNCTFC ADQKAMGKDD FTKIPNGVNG
360 370 380 390 400
VEDRMSIVWE NGVNTGKLTW CQFVRATSSE AARIFNIYPR KGRIDVGCDG
410 420 430 440 450
DIVIWDPNQS KTISKDTHHH AVDFNIFEGI KVTGIAVTTI VAGNIVWSDN
460 470 480 490 500
KLSCVKGSGR FVPRPPFGPV FDGIEQRDKV RNELLRKVDR KPYEDDNTKN

SSK
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
AF465757 mRNA. Translation: AAO33383.1.
AAFI02000005 Genomic DNA. Translation: EAL71973.1.
RefSeqiXP_646121.1. XM_641029.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi44689.DDB_0191172.

Protein family/group databases

MEROPSiM38.973.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

dictyBaseiDDB_G0269246. pyd2.

Phylogenomic databases

eggNOGiCOG0044.
InParanoidiQ55DL0.
KOiK01464.
OMAiQHQDSLW.
PhylomeDBiQ55DL0.

Miscellaneous databases

EvolutionaryTraceiQ55DL0.
PROiQ55DL0.

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.
ProtoNetiSearch...

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: January 7, 2015
This is version 68 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

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.