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Reviewed, UniProtKB/Swiss-Prot Q55DL0 (DPYS_DICDI)

Last modified June 16, 2009. Version 30. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

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

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Protein attributes

Sequence length503 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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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.

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Ontologies

Keywords
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Molecular functiondihydropyrimidinase activity

Inferred from electronic annotation. Source: EC

zinc ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

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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...

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Sequences

Sequence LengthMass (Da)Tools
Q55DL0-1 [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

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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.

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Cross-references

Sequence databases

AF465757 mRNA. Translation: AAO33383.1.
AAFI02000005 Genomic DNA. Translation: EAL71973.1.
RefSeqXP_646121.1.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
2FTWX-ray2.05A1-503[»]
ModBaseSearch...

Protein family/group databases

MEROPSM38.973.

Genome annotation databases

GeneID3397003.
KEGGddi:DDB_0191172.

Organism-specific databases

dictyBaseDDB_G0269246. pyd2.

Phylogenomic databases

OMAQ55DL0. YEAGVFS.

Enzyme and pathway databases

BRENDA3.5.2.2. 424.

Family and domain databases

InterProIPR006680. Amidohydro_1.
IPR011778. D-hydantoinase.
[Graphical view]
PfamPF01979. Amidohydro_1. 1 hit.
[Graphical view]
ProDomPD000518. DHOase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
TIGRFAMsTIGR02033. D-hydantoinase. 1 hit.
ProtoNetSearch...

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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: June 16, 2009
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

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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

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents