DPYS_DICDI
ID DPYS_DICDI Reviewed; 503 AA.
AC Q55DL0; Q86LT2;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Dihydropyrimidinase;
DE Short=DHP;
DE Short=DHPase;
DE EC=3.5.2.2 {ECO:0000269|PubMed:12626710};
DE AltName: Full=Dihydropyrimidine amidohydrolase;
DE AltName: Full=Hydantoinase;
GN Name=pyd2; ORFNames=DDB_G0269246;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12626710; DOI=10.1093/nar/gkg258;
RA Gojkovic Z., Rislund L., Andersen B., Sandrini M.P., Cook P.F.,
RA Schnackerz K.D., Piskur J.;
RT "Dihydropyrimidine amidohydrolases and dihydroorotases share the same
RT origin and several enzymatic properties.";
RL Nucleic Acids Res. 31:1683-1692(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH ZINC IONS,
RP CARBOXYLATION AT LYS-158, AND SUBUNIT.
RX PubMed=16517602; DOI=10.1074/jbc.m513266200;
RA Lohkamp B., Andersen B., Piskur J., Dobritzsch D.;
RT "The crystal structures of dihydropyrimidinases reaffirm the close
RT relationship between cyclic amidohydrolases and explain their substrate
RT specificity.";
RL J. Biol. Chem. 281:13762-13776(2006).
CC -!- FUNCTION: Catalyzes the second step of the reductive pyrimidine
CC degradation, the reversible hydrolytic ring opening of
CC dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil
CC to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino
CC isobutyrate. {ECO:0000269|PubMed:12626710}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouracil + H2O = 3-(carbamoylamino)propanoate + H(+);
CC Xref=Rhea:RHEA:16121, ChEBI:CHEBI:11892, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15901; EC=3.5.2.2;
CC Evidence={ECO:0000269|PubMed:12626710};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16517602};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000269|PubMed:16517602};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16517602}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two zinc ions.
CC {ECO:0000269|PubMed:16517602}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {ECO:0000305}.
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DR EMBL; AF465757; AAO33383.1; -; mRNA.
DR EMBL; AAFI02000005; EAL71973.1; -; Genomic_DNA.
DR RefSeq; XP_646121.1; XM_641029.1.
DR PDB; 2FTW; X-ray; 2.05 A; A=1-503.
DR PDBsum; 2FTW; -.
DR AlphaFoldDB; Q55DL0; -.
DR SMR; Q55DL0; -.
DR STRING; 44689.DDB0191172; -.
DR MEROPS; M38.973; -.
DR PaxDb; Q55DL0; -.
DR EnsemblProtists; EAL71973; EAL71973; DDB_G0269246.
DR GeneID; 8617070; -.
DR KEGG; ddi:DDB_G0269246; -.
DR dictyBase; DDB_G0269246; pyd2.
DR eggNOG; KOG2584; Eukaryota.
DR HOGENOM; CLU_015572_2_2_1; -.
DR InParanoid; Q55DL0; -.
DR OMA; SAETHHM; -.
DR PhylomeDB; Q55DL0; -.
DR BRENDA; 3.5.2.2; 1939.
DR Reactome; R-DDI-73621; Pyrimidine catabolism.
DR EvolutionaryTrace; Q55DL0; -.
DR PRO; PR:Q55DL0; -.
DR Proteomes; UP000002195; Chromosome 1.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0004157; F:dihydropyrimidinase activity; IDA:dictyBase.
DR GO; GO:0008270; F:zinc ion binding; IDA:dictyBase.
DR GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IDA:dictyBase.
DR CDD; cd01314; D-HYD; 1.
DR DisProt; DP02958; -.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR011778; Hydantoinase/dihydroPyrase.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR Pfam; PF01979; Amidohydro_1; 1.
DR SUPFAM; SSF51338; SSF51338; 2.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR02033; D-hydantoinase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..503
FT /note="Dihydropyrimidinase"
FT /id="PRO_0000312734"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 158
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 158
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 191
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 247
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 325
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT BINDING 346
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT MOD_RES 158
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:16517602,
FT ECO:0007744|PDB:2FTW"
FT CONFLICT 381
FT /note="A -> R (in Ref. 1; AAO33383)"
FT /evidence="ECO:0000305"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 62..67
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 82..91
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 94..101
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 109..121
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 125..133
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 139..151
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 164..167
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 171..184
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 187..191
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 195..207
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 214..219
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 223..239
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 251..262
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 267..269
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 273..277
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 280..284
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 288..292
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 306..315
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 331..334
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 341..343
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 354..362
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 363..366
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 370..377
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 379..384
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 388..390
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 402..412
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 415..417
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 421..423
FT /evidence="ECO:0007829|PDB:2FTW"
FT TURN 426..429
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 431..441
FT /evidence="ECO:0007829|PDB:2FTW"
FT STRAND 444..448
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 469..471
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 474..481
FT /evidence="ECO:0007829|PDB:2FTW"
FT HELIX 483..486
FT /evidence="ECO:0007829|PDB:2FTW"
SQ SEQUENCE 503 AA; 56032 MW; 8E75DBD49100C553 CRC64;
MLRVDQTGTI LIKNGTVVND DRYFKSDVLV ENGIIKEISK NIEPKEGIKV VDATDKLLLP
GGIDTHTHFQ LPFMGTVSVD DFDIGTQAAV AGGTTFIIDF VIPTRGQSLL EAYDQWKKWA
DEKVNCDYSL HVAITWWSEQ VSREMEILVK ERGVNSFKCF MAYKNSFMVT DQEMYHIFKR
CKELGAIAQV HAENGDMVFE GQKKMLEMGI TGPEGHELSR PEALEAEATN RAIVIADSVC
TPVYIVHVQS IGAADVICKH RKEGVRVYGE PIAAGLGVDG SHMWNHDWRH AAAFVMGPPI
RPDPRTKGVL MDYLARGDLD CVGTDNCTFC ADQKAMGKDD FTKIPNGVNG VEDRMSIVWE
NGVNTGKLTW CQFVRATSSE AARIFNIYPR KGRIDVGCDG DIVIWDPNQS KTISKDTHHH
AVDFNIFEGI KVTGIAVTTI VAGNIVWSDN KLSCVKGSGR FVPRPPFGPV FDGIEQRDKV
RNELLRKVDR KPYEDDNTKN SSK
