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Reviewed, UniProtKB/Swiss-Prot Q9P903 (DPYS_SACKL)

Last modified March 3, 2009. Version 39. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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):
    5,6-dihydropyrimidine amidohydrolase
    Hydantoinase
Gene names
Name: PYD2
OrganismSaccharomyces kluyveri (Yeast) (Saccharomyces silvestris)
Taxonomic identifier4934 [NCBI]
Taxonomic lineageEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Lachancea

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Protein attributes

Sequence length542 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.1 Ref.2

Induction

Up-regulated by dihydrouracil and N-carbamyl-beta-alanine. Detectable only in cells grown on dihydrouracil and N-carbamyl-beta-alanine as sole nitrogen source. Ref.1

Post-translational modification

Carbamylation allows a single lysine to coordinate two zinc ions.

Sequence similarities

Belongs to the DHOase family. Hydantoinase/dihydropyrimidinase subfamily.

biophysicochemical properties

Kinetic parameters:

KM=0.6 mM for dihydrouracil

KM=0.235 mM for dihydrothymine

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Ontologies

Keywords
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   Technical term3D-structure
Direct protein sequencing
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 – 542542Dihydropyrimidinase
PRO_0000313804

Sites

Metal binding621Zinc 1
Metal binding641Zinc 1
Metal binding1671Zinc 1; via carbamate group
Metal binding1671Zinc 2; via carbamate group
Metal binding1991Zinc 2
Metal binding2551Zinc 2
Metal binding3581Zinc 1
Binding site1721Substrate
Binding site3311Substrate; via amide nitrogen and carbonyl oxygen
Binding site3921Substrate; via carbonyl oxygen

Amino acid modifications

Modified residue1671N6-carboxylysine

Secondary structure

1 ...................................................................................................... 542
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
Q9P903-1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: E8758452CBE86E98

FASTA54260,240
        10         20         30         40         50         60 
MPIYDLIIKN GIICTASDIY AAEIAVNNGK VQLIAASIDP SLGSEVIDAE GAFITPGGID 

        70         80         90        100        110        120 
AHVHVDEPLK LLGDVVDTME HATRSAVAGG TTTVVAFSTQ DVSKKGPSAL AESVKLDVDE 

       130        140        150        160        170        180 
YSEQTLYCDY GLHLILFQIE KPSVEARELL DVQLQAAYND YGVSSVKMFM TYPGLQISDY 

       190        200        210        220        230        240 
DIMSAMYATR KNGFTTMLHA ENGDMVKWMI EALEEQGLTD AYYHGVSRPS IVEGEATNRA 

       250        260        270        280        290        300 
ITLATTMDTP ILFVHVSSPQ AAEVIKQAQT KGLKVYAETC PQYALLSDAI TRCHHHGEVE 

       310        320        330        340        350        360 
SYGVGIDLSS ISESPFTNPD DRFIGSKYIC SPPIRPEGTQ KSIWKGMNNG TFTIVGSDHC 

       370        380        390        400        410        420 
SYNYYEKTST ASKHRAFDPE NNKNGEFRYI PNGLPGVCTR MPLLYDYGYL RGNLTSMMKL 

       430        440        450        460        470        480 
VEIQCTNPAK VYGMYPQKGS ILPGVSDADL VIWYPDDSKK EYNSKPKLIT NKLMEHNCDY 

       490        500        510        520        530        540 
TPFEGIEIKN WPRYTIVKGK IVYKEGEILK ENADGKYLKR GKSFMCTPKN EWVTEWRPKY 


ES

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References

[1]"PYD2 encodes 5,6-dihydropyrimidine amidohydrolase, which participates in a novel fungal catabolic pathway."
Gojkovic Z., Jahnke K., Schnackerz K.D., Piskur J.
J. Mol. Biol. 295:1073-1087(2000) [PubMed: 10656811] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-11, FUNCTION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION.
Strain: ATCC 58438 / CBS 3082 / IFO 1685 / JCM 7257 / NRRL Y-12651.
[2]"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 (2.4 ANGSTROMS) IN COMPLEXES WITH ZINC IONS; SUBSTRATE AND PRODUCT, CARBAMYLATION AT LYS-167, SUBUNIT.

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Cross-references

Sequence databases

AF156967 Genomic DNA. Translation: AAF69237.1.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
2FTYX-ray2.40A/B/C/D2-542[»]
2FVKX-ray2.40A/B/C/D2-542[»]
2FVMX-ray2.45A/B/C/D2-542[»]
ModBaseSearch...

Enzyme and pathway databases

BRENDA3.5.2.2. 274780.

Family and domain databases

InterProIPR006680. Amidohydro_1.
[Graphical view]
PfamPF01979. Amidohydro_1. 2 hits.
[Graphical view]
ProDomPD000518. DHOase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
ProtoNetSearch...

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Entry information

Entry nameDPYS_SACKL
AccessionPrimary (citable) accession number: Q9P903
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 1, 2000
Last modified: March 3, 2009
This is version 39 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectFPAP (Fungal Proteome Annotation Project)

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Relevant documents

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