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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.1 Publication

Cofactori

Zn2+1 PublicationNote: Binds 2 Zn2+ ions per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi66Zinc 1Combined sources1 Publication1
Metal bindingi68Zinc 1Combined sources1 Publication1
Metal bindingi158Zinc 1; via carbamate groupCombined sources1 Publication1
Metal bindingi158Zinc 2; via carbamate groupCombined sources1 Publication1
Binding sitei163SubstrateBy similarity1
Metal bindingi191Zinc 2Combined sources1 Publication1
Metal bindingi247Zinc 2Combined sources1 Publication1
Metal bindingi325Zinc 1Combined sources1 Publication1
Binding sitei346Substrate; via carbonyl oxygenBy similarity1

GO - Molecular functioni

  • dihydropyrimidinase activity Source: dictyBase
  • zinc ion binding Source: dictyBase

GO - Biological processi

  • pyrimidine nucleobase catabolic process Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.2.2. 1939.
ReactomeiR-DDI-73621. Pyrimidine catabolism.

Protein family/group databases

MEROPSiM38.973.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydropyrimidinase (EC:3.5.2.21 Publication)
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
Proteomesi
  • UP000002195 Componentsi: Chromosome 1, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0269246. pyd2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003127341 – 503DihydropyrimidinaseAdd BLAST503

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei158N6-carboxylysineCombined sources1 Publication1

Post-translational modificationi

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

Proteomic databases

PaxDbiQ55DL0.
PRIDEiQ55DL0.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi44689.DDB0191172.

Structurei

Secondary structure

1503
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 14Combined sources5
Beta strandi16 – 18Combined sources3
Beta strandi23 – 25Combined sources3
Beta strandi27 – 31Combined sources5
Beta strandi34 – 40Combined sources7
Beta strandi50 – 52Combined sources3
Beta strandi57 – 60Combined sources4
Beta strandi62 – 67Combined sources6
Helixi82 – 91Combined sources10
Beta strandi94 – 101Combined sources8
Helixi109 – 121Combined sources13
Beta strandi125 – 133Combined sources9
Helixi139 – 151Combined sources13
Beta strandi156 – 162Combined sources7
Turni164 – 167Combined sources4
Helixi171 – 184Combined sources14
Beta strandi187 – 191Combined sources5
Helixi195 – 207Combined sources13
Helixi214 – 219Combined sources6
Helixi223 – 239Combined sources17
Beta strandi243 – 245Combined sources3
Helixi251 – 262Combined sources12
Beta strandi267 – 269Combined sources3
Helixi273 – 277Combined sources5
Helixi280 – 284Combined sources5
Helixi288 – 292Combined sources5
Helixi306 – 315Combined sources10
Helixi331 – 334Combined sources4
Helixi335 – 337Combined sources3
Helixi341 – 343Combined sources3
Turni351 – 353Combined sources3
Helixi354 – 362Combined sources9
Turni363 – 366Combined sources4
Helixi370 – 377Combined sources8
Helixi379 – 384Combined sources6
Turni388 – 390Combined sources3
Beta strandi402 – 412Combined sources11
Turni415 – 417Combined sources3
Beta strandi421 – 423Combined sources3
Turni426 – 429Combined sources4
Beta strandi431 – 441Combined sources11
Beta strandi444 – 448Combined sources5
Helixi469 – 471Combined sources3
Helixi474 – 481Combined sources8
Helixi483 – 486Combined sources4

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ55DL0.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2584. Eukaryota.
COG0044. LUCA.
InParanoidiQ55DL0.
KOiK01464.
OMAiFHMAVTW.
PhylomeDBiQ55DL0.

Family and domain databases

CDDicd01314. D-HYD. 1 hit.
Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro-rel.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
IPR032466. Metal_Hydrolase.
[Graphical view]
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
SSF51556. SSF51556. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti381A → R in AAO33383 (PubMed:12626710).Curated1

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

EnsemblProtistsiEAL71973; EAL71973; 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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FTWX-ray2.05A1-503[»]
ProteinModelPortaliQ55DL0.
SMRiQ55DL0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0191172.

Protein family/group databases

MEROPSiM38.973.

Proteomic databases

PaxDbiQ55DL0.
PRIDEiQ55DL0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiEAL71973; EAL71973; DDB_G0269246.
GeneIDi8617070.
KEGGiddi:DDB_G0269246.

Organism-specific databases

dictyBaseiDDB_G0269246. pyd2.

Phylogenomic databases

eggNOGiKOG2584. Eukaryota.
COG0044. LUCA.
InParanoidiQ55DL0.
KOiK01464.
OMAiFHMAVTW.
PhylomeDBiQ55DL0.

Enzyme and pathway databases

BRENDAi3.5.2.2. 1939.
ReactomeiR-DDI-73621. Pyrimidine catabolism.

Miscellaneous databases

EvolutionaryTraceiQ55DL0.
PROiQ55DL0.

Family and domain databases

CDDicd01314. D-HYD. 1 hit.
Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro-rel.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
IPR032466. Metal_Hydrolase.
[Graphical view]
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
SSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.
ProtoNetiSearch...

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: November 2, 2016
This is version 80 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

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 one 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.