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Protein

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA

Gene

preA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pyrimidine base degradation. Catalyzes physiologically the reduction of uracil to 5,6-dihydrouracil (DHU) by using NADH as a specific cosubstrate. It also catalyzes the reverse reaction and the reduction of thymine to 5,6-dihydrothymine (DHT).2 Publications

Catalytic activityi

5,6-dihydrouracil + NAD+ = uracil + NADH.1 Publication
5,6-dihydrothymine + NAD+ = thymine + NADH.1 Publication

Cofactori

[4Fe-4S] clusterCuratedNote: Binds 2 [4Fe-4S] clusters.Curated

Kineticsi

  1. KM=38 µM for uracil (at pH 6 and 30 degrees Celsius)1 Publication
  2. KM=87 µM for thymidine (at pH 6 and 30 degrees Celsius)1 Publication
  3. KM=130 µM for DHT (at pH 11 and 30 degrees Celsius)1 Publication
  4. KM=160 µM for DHU (at pH 11 and 30 degrees Celsius)1 Publication
  1. Vmax=0.18 µmol/min/mg enzyme toward DHT (at pH 11 and 30 degrees Celsius)1 Publication
  2. Vmax=0.26 µmol/min/mg enzyme toward thymidine (at pH 6 and 30 degrees Celsius)1 Publication
  3. Vmax=0.43 µmol/min/mg enzyme toward uracil (at pH 6 and 30 degrees Celsius)1 Publication
  4. Vmax=0.44 µmol/min/mg enzyme toward DHU (at pH 11 and 30 degrees Celsius)1 Publication
  5. Vmax=0.67 µmol/min/mg enzyme toward fluorouracil (at pH 6 and 30 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei76 – 761SubstrateBy similarity
Active sitei137 – 1371NucleophileBy similarity
Metal bindingi344 – 3441Iron-sulfur 1 (4Fe-4S)Sequence analysis
Metal bindingi347 – 3471Iron-sulfur 1 (4Fe-4S)Sequence analysis
Metal bindingi350 – 3501Iron-sulfur 1 (4Fe-4S)Sequence analysis
Metal bindingi354 – 3541Iron-sulfur 2 (4Fe-4S)Sequence analysis
Metal bindingi378 – 3781Iron-sulfur 2 (4Fe-4S)Sequence analysis
Metal bindingi381 – 3811Iron-sulfur 2 (4Fe-4S)Sequence analysis
Metal bindingi384 – 3841Iron-sulfur 2 (4Fe-4S)Sequence analysis
Metal bindingi388 – 3881Iron-sulfur 1 (4Fe-4S)Sequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

BioCyciEcoCyc:EG11289-MONOMER.
ECOL316407:JW2134-MONOMER.
MetaCyc:EG11289-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA (EC:1.3.1.1)
Short name:
DPD
Alternative name(s):
Dihydrothymine dehydrogenase
Dihydrouracil dehydrogenase
Gene namesi
Name:preA
Synonyms:yeiA
Ordered Locus Names:b2147, JW2134
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11289. preA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 411411NAD-dependent dihydropyrimidine dehydrogenase subunit PreAPRO_0000169148Add
BLAST

Proteomic databases

PaxDbiP25889.

Expressioni

Inductioni

Transcriptionally regulated by IscS.1 Publication

Interactioni

Subunit structurei

Heterotetramer of 2 PreA and 2 PreT subunits.1 Publication

Protein-protein interaction databases

BioGridi4259170. 9 interactions.
DIPiDIP-11915N.
IntActiP25889. 2 interactions.
STRINGi511145.b2147.

Structurei

3D structure databases

ProteinModelPortaliP25889.
SMRiP25889. Positions 5-395.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini335 – 367334Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
BLAST
Domaini369 – 398304Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni134 – 1363Substrate bindingBy similarity
Regioni201 – 2022Substrate bindingBy similarity

Sequence similaritiesi

Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4107SJI. Bacteria.
COG0167. LUCA.
COG1146. LUCA.
HOGENOMiHOG000225106.
InParanoidiP25889.
KOiK17723.
OMAiMVPCVEE.
OrthoDBiEOG6NPM9S.
PhylomeDBiP25889.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25889-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTKDLSITF CGVKFPNPFC LSSSPVGNCY EMCAKAYDTG WGGVVFKTIG
60 70 80 90 100
FFIANEVSPR FDHLVKEDTG FIGFKNMEQI AEHPLEENLA ALRRLKEDYP
110 120 130 140 150
DKVLIASIMG ENEQQWEELA RLVQEAGADM IECNFSCPQM TSHAMGSDVG
160 170 180 190 200
QSPELVEKYC RAVKRGSTLP MLAKMTPNIG DMCEVALAAK RGGADGIAAI
210 220 230 240 250
NTVKSITNID LNQKIGMPIV NGKSSISGYS GKAVKPIALR FIQQMRTHPE
260 270 280 290 300
LRDFPISGIG GIETWEDAAE FLLLGAATLQ VTTGIMQYGY RIVEDMASGL
310 320 330 340 350
SHYLADQGFD SLQEMVGLAN NNIVPAEDLD RSYIVYPRIN LDKCVGCGRC
360 370 380 390 400
YISCYDGGHQ AMEWSEKTRT PHCNTEKCVG CLLCGHVCPV GCIELGEVKF
410
KKGEKEHPVT L
Length:411
Mass (Da):45,069
Last modified:July 15, 1998 - v3
Checksum:iF44F5F7BA8FAD23C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti389 – 41123PVGCI…HPVTL → RWVVLSSGK in M59444 (PubMed:1719366).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75208.2.
AP009048 Genomic DNA. Translation: BAE76624.1.
M59444 Genomic DNA. No translation available.
RefSeqiNP_416652.4. NC_000913.3.
WP_000956071.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75208; AAC75208; b2147.
BAE76624; BAE76624; BAE76624.
GeneIDi949037.
KEGGiecj:JW2134.
eco:b2147.
PATRICi32119637. VBIEscCol129921_2229.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75208.2.
AP009048 Genomic DNA. Translation: BAE76624.1.
M59444 Genomic DNA. No translation available.
RefSeqiNP_416652.4. NC_000913.3.
WP_000956071.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP25889.
SMRiP25889. Positions 5-395.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259170. 9 interactions.
DIPiDIP-11915N.
IntActiP25889. 2 interactions.
STRINGi511145.b2147.

Proteomic databases

PaxDbiP25889.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75208; AAC75208; b2147.
BAE76624; BAE76624; BAE76624.
GeneIDi949037.
KEGGiecj:JW2134.
eco:b2147.
PATRICi32119637. VBIEscCol129921_2229.

Organism-specific databases

EchoBASEiEB1266.
EcoGeneiEG11289. preA.

Phylogenomic databases

eggNOGiENOG4107SJI. Bacteria.
COG0167. LUCA.
COG1146. LUCA.
HOGENOMiHOG000225106.
InParanoidiP25889.
KOiK17723.
OMAiMVPCVEE.
OrthoDBiEOG6NPM9S.
PhylomeDBiP25889.

Enzyme and pathway databases

BioCyciEcoCyc:EG11289-MONOMER.
ECOL316407:JW2134-MONOMER.
MetaCyc:EG11289-MONOMER.

Miscellaneous databases

PROiP25889.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Nucleotide sequence and analysis of the mgl operon of Escherichia coli K12."
    Hogg R.W., Voelker C., von Carlowitz I.
    Mol. Gen. Genet. 229:453-459(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 313-411.
    Strain: K12.
  4. "The iscS gene deficiency affects the expression of pyrimidine metabolism genes."
    Mihara H., Hidese R., Yamane M., Kurihara T., Esaki N.
    Biochem. Biophys. Res. Commun. 372:407-411(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-15, FUNCTION IN PYRIMIDINE METABOLISM, INDUCTION, IRON-SULFUR, NAD.
  5. "Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil."
    Hidese R., Mihara H., Kurihara T., Esaki N.
    J. Bacteriol. 193:989-993(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DIHYDROPYRIMIDINE DEHYDROGENASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Entry informationi

Entry nameiPREA_ECOLI
AccessioniPrimary (citable) accession number: P25889
Secondary accession number(s): P76441, Q2MAT2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 15, 1998
Last modified: June 8, 2016
This is version 136 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.