PREA_ECOLI
ID PREA_ECOLI Reviewed; 411 AA.
AC P25889; P76441; Q2MAT2;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 3.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
DE Short=DPD;
DE EC=1.3.1.1;
DE AltName: Full=Dihydrothymine dehydrogenase;
DE AltName: Full=Dihydrouracil dehydrogenase;
GN Name=preA; Synonyms=yeiA; OrderedLocusNames=b2147, JW2134;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 313-411.
RC STRAIN=K12;
RX PubMed=1719366; DOI=10.1007/bf00267469;
RA Hogg R.W., Voelker C., von Carlowitz I.;
RT "Nucleotide sequence and analysis of the mgl operon of Escherichia coli
RT K12.";
RL Mol. Gen. Genet. 229:453-459(1991).
RN [4]
RP PROTEIN SEQUENCE OF 1-15, FUNCTION IN PYRIMIDINE METABOLISM, INDUCTION,
RP IRON-SULFUR, AND NAD.
RX PubMed=18482579; DOI=10.1016/j.bbrc.2008.05.019;
RA Mihara H., Hidese R., Yamane M., Kurihara T., Esaki N.;
RT "The iscS gene deficiency affects the expression of pyrimidine metabolism
RT genes.";
RL Biochem. Biophys. Res. Commun. 372:407-411(2008).
RN [5]
RP FUNCTION AS A DIHYDROPYRIMIDINE DEHYDROGENASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=21169495; DOI=10.1128/jb.01178-10;
RA Hidese R., Mihara H., Kurihara T., Esaki N.;
RT "Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent
RT heterotetramer essential for the production of 5,6-dihydrouracil.";
RL J. Bacteriol. 193:989-993(2011).
CC -!- FUNCTION: Involved in pyrimidine base degradation. Catalyzes
CC physiologically the reduction of uracil to 5,6-dihydrouracil (DHU) by
CC using NADH as a specific cosubstrate. It also catalyzes the reverse
CC reaction and the reduction of thymine to 5,6-dihydrothymine (DHT).
CC {ECO:0000269|PubMed:18482579, ECO:0000269|PubMed:21169495}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouracil + NAD(+) = H(+) + NADH + uracil;
CC Xref=Rhea:RHEA:20189, ChEBI:CHEBI:15378, ChEBI:CHEBI:15901,
CC ChEBI:CHEBI:17568, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.3.1.1;
CC Evidence={ECO:0000269|PubMed:21169495};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrothymine + NAD(+) = H(+) + NADH + thymine;
CC Xref=Rhea:RHEA:28791, ChEBI:CHEBI:15378, ChEBI:CHEBI:17821,
CC ChEBI:CHEBI:27468, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.3.1.1;
CC Evidence={ECO:0000269|PubMed:21169495};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000305};
CC Note=Binds 2 [4Fe-4S] clusters. {ECO:0000305};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=38 uM for uracil (at pH 6 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:21169495};
CC KM=87 uM for thymidine (at pH 6 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:21169495};
CC KM=130 uM for DHT (at pH 11 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:21169495};
CC KM=160 uM for DHU (at pH 11 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:21169495};
CC Vmax=0.18 umol/min/mg enzyme toward DHT (at pH 11 and 30 degrees
CC Celsius) {ECO:0000269|PubMed:21169495};
CC Vmax=0.26 umol/min/mg enzyme toward thymidine (at pH 6 and 30 degrees
CC Celsius) {ECO:0000269|PubMed:21169495};
CC Vmax=0.43 umol/min/mg enzyme toward uracil (at pH 6 and 30 degrees
CC Celsius) {ECO:0000269|PubMed:21169495};
CC Vmax=0.44 umol/min/mg enzyme toward DHU (at pH 11 and 30 degrees
CC Celsius) {ECO:0000269|PubMed:21169495};
CC Vmax=0.67 umol/min/mg enzyme toward fluorouracil (at pH 6 and 30
CC degrees Celsius) {ECO:0000269|PubMed:21169495};
CC -!- SUBUNIT: Heterotetramer of 2 PreA and 2 PreT subunits.
CC {ECO:0000269|PubMed:21169495}.
CC -!- INDUCTION: Transcriptionally regulated by IscS.
CC {ECO:0000269|PubMed:18482579}.
CC -!- SIMILARITY: Belongs to the dihydropyrimidine dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC75208.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE76624.1; -; Genomic_DNA.
DR EMBL; M59444; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_416652.4; NC_000913.3.
DR RefSeq; WP_000956071.1; NZ_SSZK01000011.1.
DR AlphaFoldDB; P25889; -.
DR SMR; P25889; -.
DR BioGRID; 4259170; 34.
DR BioGRID; 853281; 1.
DR ComplexPortal; CPX-5561; NAD-dependent dihydropyrimidine dehydrogenase complex.
DR DIP; DIP-11915N; -.
DR IntAct; P25889; 2.
DR STRING; 511145.b2147; -.
DR jPOST; P25889; -.
DR PaxDb; P25889; -.
DR PRIDE; P25889; -.
DR EnsemblBacteria; AAC75208; AAC75208; b2147.
DR EnsemblBacteria; BAE76624; BAE76624; BAE76624.
DR GeneID; 949037; -.
DR KEGG; ecj:JW2134; -.
DR KEGG; eco:b2147; -.
DR PATRIC; fig|1411691.4.peg.95; -.
DR EchoBASE; EB1266; -.
DR eggNOG; COG0167; Bacteria.
DR eggNOG; COG1146; Bacteria.
DR HOGENOM; CLU_042042_4_2_6; -.
DR InParanoid; P25889; -.
DR OMA; MVPCVEE; -.
DR PhylomeDB; P25889; -.
DR BioCyc; EcoCyc:EG11289-MON; -.
DR BioCyc; MetaCyc:EG11289-MON; -.
DR SABIO-RK; P25889; -.
DR PRO; PR:P25889; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:1990204; C:oxidoreductase complex; IDA:ComplexPortal.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0004159; F:dihydropyrimidine dehydrogenase (NAD+) activity; IEA:UniProtKB-EC.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003954; F:NADH dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0002058; F:uracil binding; IBA:GO_Central.
DR GO; GO:0071978; P:bacterial-type flagellum-dependent swarming motility; IMP:EcoCyc.
DR GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IDA:UniProtKB.
DR GO; GO:0006210; P:thymine catabolic process; IDA:ComplexPortal.
DR GO; GO:0006212; P:uracil catabolic process; IDA:ComplexPortal.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR044512; DPYD.
DR PANTHER; PTHR43073; PTHR43073; 2.
DR Pfam; PF01180; DHO_dh; 1.
DR TIGRFAMs; TIGR01037; pyrD_sub1_fam; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 1.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
PE 1: Evidence at protein level;
KW 4Fe-4S; Direct protein sequencing; Iron; Iron-sulfur; Metal-binding; NAD;
KW Oxidoreductase; Reference proteome; Repeat.
FT CHAIN 1..411
FT /note="NAD-dependent dihydropyrimidine dehydrogenase
FT subunit PreA"
FT /id="PRO_0000169148"
FT DOMAIN 335..367
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 369..398
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT ACT_SITE 137
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 76
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 134..136
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 201..202
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 344
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 347
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 350
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 354
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 378
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 381
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 384
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 388
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT CONFLICT 389..411
FT /note="PVGCIELGEVKFKKGEKEHPVTL -> RWVVLSSGK (in Ref. 3;
FT M59444)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 411 AA; 45069 MW; F44F5F7BA8FAD23C CRC64;
MLTKDLSITF CGVKFPNPFC LSSSPVGNCY EMCAKAYDTG WGGVVFKTIG FFIANEVSPR
FDHLVKEDTG FIGFKNMEQI AEHPLEENLA ALRRLKEDYP DKVLIASIMG ENEQQWEELA
RLVQEAGADM IECNFSCPQM TSHAMGSDVG QSPELVEKYC RAVKRGSTLP MLAKMTPNIG
DMCEVALAAK RGGADGIAAI NTVKSITNID LNQKIGMPIV NGKSSISGYS GKAVKPIALR
FIQQMRTHPE LRDFPISGIG GIETWEDAAE FLLLGAATLQ VTTGIMQYGY RIVEDMASGL
SHYLADQGFD SLQEMVGLAN NNIVPAEDLD RSYIVYPRIN LDKCVGCGRC YISCYDGGHQ
AMEWSEKTRT PHCNTEKCVG CLLCGHVCPV GCIELGEVKF KKGEKEHPVT L
