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Q55DL0 (DPYS_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 48. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Dihydropyrimidinase
Short name=DHP
Short name=DHPase
EC=3.5.2.2
Alternative name(s):
Dihydropyrimidine amidohydrolase
Hydantoinase
Gene names
Name:pyd2
ORF Names:DDB_G0269246
OrganismDictyostelium discoideum (Slime mold)
Taxonomic identifier44689 [NCBI]
Taxonomic lineageEukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length503 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Cofactor

Binds 2 zinc ions per subunit.

Subunit structure

Homotetramer. Ref.3

Post-translational modification

Carbamylation allows a single lysine to coordinate two zinc ions.

Sequence similarities

Belongs to the DHOase family. Hydantoinase/dihydropyrimidinase subfamily.

Ontologies

Keywords
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological processpyrimidine base catabolic process

Inferred from direct assay Ref.1. Source: dictyBase

   Cellular componentcytoplasm

Inferred from electronic annotation. Source: InterPro

extracellular space

Inferred from direct assay. Source: dictyBase

   Molecular functiondihydropyrimidinase activity

Inferred from direct assay Ref.1. Source: dictyBase

zinc ion binding

Inferred from direct assay Ref.1. Source: dictyBase

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 503503Dihydropyrimidinase
PRO_0000312734

Sites

Metal binding661Zinc 1
Metal binding681Zinc 1
Metal binding1581Zinc 1; via carbamate group
Metal binding1581Zinc 2; via carbamate group
Metal binding1911Zinc 2
Metal binding2471Zinc 2
Metal binding3251Zinc 1
Binding site1631Substrate By similarity
Binding site3461Substrate; via carbonyl oxygen By similarity

Amino acid modifications

Modified residue1581N6-carboxylysine

Experimental info

Sequence conflict3811A → R in AAO33383. Ref.1

Secondary structure

1 ........................................................................................ 503
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q55DL0 [UniParc].

Last modified May 24, 2005. Version 1.
Checksum: 8E75DBD49100C553

FASTA50356,032
        10         20         30         40         50         60 
MLRVDQTGTI LIKNGTVVND DRYFKSDVLV ENGIIKEISK NIEPKEGIKV VDATDKLLLP 

        70         80         90        100        110        120 
GGIDTHTHFQ LPFMGTVSVD DFDIGTQAAV AGGTTFIIDF VIPTRGQSLL EAYDQWKKWA 

       130        140        150        160        170        180 
DEKVNCDYSL HVAITWWSEQ VSREMEILVK ERGVNSFKCF MAYKNSFMVT DQEMYHIFKR 

       190        200        210        220        230        240 
CKELGAIAQV HAENGDMVFE GQKKMLEMGI TGPEGHELSR PEALEAEATN RAIVIADSVC 

       250        260        270        280        290        300 
TPVYIVHVQS IGAADVICKH RKEGVRVYGE PIAAGLGVDG SHMWNHDWRH AAAFVMGPPI 

       310        320        330        340        350        360 
RPDPRTKGVL MDYLARGDLD CVGTDNCTFC ADQKAMGKDD FTKIPNGVNG VEDRMSIVWE 

       370        380        390        400        410        420 
NGVNTGKLTW CQFVRATSSE AARIFNIYPR KGRIDVGCDG DIVIWDPNQS KTISKDTHHH 

       430        440        450        460        470        480 
AVDFNIFEGI KVTGIAVTTI VAGNIVWSDN KLSCVKGSGR FVPRPPFGPV FDGIEQRDKV 

       490        500 
RNELLRKVDR KPYEDDNTKN SSK

« Hide

References

« Hide 'large scale' references
[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: 12626710] [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. expand/collapse author list , 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: 15875012] [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: 16517602] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH ZINC IONS, CARBAMYLATION AT LYS-158, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AF465757 mRNA. Translation: AAO33383.1.
AAFI02000005 Genomic DNA. Translation: EAL71973.1.
RefSeqXP_646121.1. XM_641029.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FTWX-ray2.05A1-503[»]
ProteinModelPortalQ55DL0.
SMRQ55DL0. Positions 7-490.
ModBaseSearch...

Protein-protein interaction databases

STRINGQ55DL0.

Protein family/group databases

MEROPSM38.973.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsDDB0191172; DDB0191172; DDB_G0269246.
GeneID8617070.
GenomeReviewsGene locus pyd2 in contig CM000150_GR.
KEGGddi:DDB_G0269246.

Organism-specific databases

dictyBaseDDB_G0269246. pyd2.

Phylogenomic databases

eggNOGKOG2584.
GeneTreeEPrGT00050000004629.
HOGENOMHBG724623.
OMAKSASDYG.
PhylomeDBQ55DL0.
ProtClustDBCLSZ2497287.

Family and domain databases

InterProIPR006680. Amidohydro_1.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
[Graphical view]
KOK01464.
PfamPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMSSF51338. Metalo_hydrolase. 2 hits.
TIGRFAMsTIGR02033. D-hydantoinase. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDPYS_DICDI
AccessionPrimary (citable) accession number: Q55DL0
Secondary accession number(s): Q86LT2
Entry history
Integrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: May 24, 2005
Last modified: November 16, 2011
This is version 48 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

Relevant documents

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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