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UniProtKB - P25889 (PREA_ECOLI)
Protein
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA
Gene
preA
Organism
Escherichia coli (strain K12)
Status
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 PublicationsCatalytic activityi
Cofactori
[4Fe-4S] clusterCuratedNote: Binds 2 [4Fe-4S] clusters.Curated
Kineticsi
- KM=38 µM for uracil (at pH 6 and 30 degrees Celsius)1 Publication
- KM=87 µM for thymidine (at pH 6 and 30 degrees Celsius)1 Publication
- KM=130 µM for DHT (at pH 11 and 30 degrees Celsius)1 Publication
- KM=160 µM for DHU (at pH 11 and 30 degrees Celsius)1 Publication
- Vmax=0.18 µmol/min/mg enzyme toward DHT (at pH 11 and 30 degrees Celsius)1 Publication
- Vmax=0.26 µmol/min/mg enzyme toward thymidine (at pH 6 and 30 degrees Celsius)1 Publication
- Vmax=0.43 µmol/min/mg enzyme toward uracil (at pH 6 and 30 degrees Celsius)1 Publication
- Vmax=0.44 µmol/min/mg enzyme toward DHU (at pH 11 and 30 degrees Celsius)1 Publication
- Vmax=0.67 µmol/min/mg enzyme toward fluorouracil (at pH 6 and 30 degrees Celsius)1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 76 | SubstrateBy similarity | 1 | |
Active sitei | 137 | NucleophileBy similarity | 1 | |
Metal bindingi | 344 | Iron-sulfur (4Fe-4S) 1Sequence analysis | 1 | |
Metal bindingi | 347 | Iron-sulfur (4Fe-4S) 1Sequence analysis | 1 | |
Metal bindingi | 350 | Iron-sulfur (4Fe-4S) 1Sequence analysis | 1 | |
Metal bindingi | 354 | Iron-sulfur (4Fe-4S) 2Sequence analysis | 1 | |
Metal bindingi | 378 | Iron-sulfur (4Fe-4S) 2Sequence analysis | 1 | |
Metal bindingi | 381 | Iron-sulfur (4Fe-4S) 2Sequence analysis | 1 | |
Metal bindingi | 384 | Iron-sulfur (4Fe-4S) 2Sequence analysis | 1 | |
Metal bindingi | 388 | Iron-sulfur (4Fe-4S) 1Sequence analysis | 1 |
GO - Molecular functioni
- 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
- dihydropyrimidine dehydrogenase (NAD+) activity Source: UniProtKB-EC
- iron-sulfur cluster binding Source: EcoCyc
- metal ion binding Source: UniProtKB-KW
- NADH dehydrogenase activity Source: UniProtKB
- NADP binding Source: GO_Central
- uracil binding Source: GO_Central
GO - Biological processi
- pyrimidine nucleobase catabolic process Source: UniProtKB
- thymine catabolic process Source: ComplexPortal
- uracil catabolic process Source: ComplexPortal
Keywordsi
Molecular function | Oxidoreductase |
Ligand | 4Fe-4S, Iron, Iron-sulfur, Metal-binding, NAD |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11289-MONOMER |
SABIO-RKi | P25889 |
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 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
Other locations
- cytoplasm Source: InterPro
- oxidoreductase complex Source: ComplexPortal
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000169148 | 1 – 411 | NAD-dependent dihydropyrimidine dehydrogenase subunit PreAAdd BLAST | 411 |
Proteomic databases
jPOSTi | P25889 |
PaxDbi | P25889 |
PRIDEi | P25889 |
Expressioni
Inductioni
Transcriptionally regulated by IscS.1 Publication
Interactioni
Subunit structurei
Heterotetramer of 2 PreA and 2 PreT subunits.
1 PublicationProtein-protein interaction databases
BioGRIDi | 4259170, 34 interactors 853281, 1 interactor |
ComplexPortali | CPX-5561, NAD-dependent dihydropyrimidine dehydrogenase complex |
DIPi | DIP-11915N |
IntActi | P25889, 2 interactors |
STRINGi | 511145.b2147 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 335 – 367 | 4Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST | 33 | |
Domaini | 369 – 398 | 4Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST | 30 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 134 – 136 | Substrate bindingBy similarity | 3 | |
Regioni | 201 – 202 | Substrate bindingBy similarity | 2 |
Sequence similaritiesi
Belongs to the dihydropyrimidine dehydrogenase family.Curated
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | COG0167, Bacteria COG1146, Bacteria |
HOGENOMi | CLU_042042_4_2_6 |
InParanoidi | P25889 |
PhylomeDBi | P25889 |
Family and domain databases
Gene3Di | 3.20.20.70, 1 hit |
InterProi | View protein in InterPro IPR017896, 4Fe4S_Fe-S-bd IPR017900, 4Fe4S_Fe_S_CS IPR013785, Aldolase_TIM IPR005720, Dihydroorotate_DH IPR044512, DPYD |
PANTHERi | PTHR43073, PTHR43073, 2 hits |
Pfami | View protein in Pfam PF01180, DHO_dh, 1 hit |
TIGRFAMsi | TIGR01037, pyrD_sub1_fam, 1 hit |
PROSITEi | View protein in PROSITE PS00198, 4FE4S_FER_1, 1 hit PS51379, 4FE4S_FER_2, 2 hits |
i Sequence
Sequence statusi: Complete.
P25889-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 389 – 411 | PVGCI…HPVTL → RWVVLSSGK in M59444 (PubMed:1719366).CuratedAdd BLAST | 23 |
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. |
RefSeqi | NP_416652.4, NC_000913.3 WP_000956071.1, NZ_SSZK01000011.1 |
Genome annotation databases
EnsemblBacteriai | AAC75208; AAC75208; b2147 BAE76624; BAE76624; BAE76624 |
GeneIDi | 949037 |
KEGGi | ecj:JW2134 eco:b2147 |
PATRICi | fig|1411691.4.peg.95 |
Similar proteinsi
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. |
RefSeqi | NP_416652.4, NC_000913.3 WP_000956071.1, NZ_SSZK01000011.1 |
3D structure databases
SMRi | P25889 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 4259170, 34 interactors 853281, 1 interactor |
ComplexPortali | CPX-5561, NAD-dependent dihydropyrimidine dehydrogenase complex |
DIPi | DIP-11915N |
IntActi | P25889, 2 interactors |
STRINGi | 511145.b2147 |
Proteomic databases
jPOSTi | P25889 |
PaxDbi | P25889 |
PRIDEi | P25889 |
Genome annotation databases
EnsemblBacteriai | AAC75208; AAC75208; b2147 BAE76624; BAE76624; BAE76624 |
GeneIDi | 949037 |
KEGGi | ecj:JW2134 eco:b2147 |
PATRICi | fig|1411691.4.peg.95 |
Organism-specific databases
EchoBASEi | EB1266 |
Phylogenomic databases
eggNOGi | COG0167, Bacteria COG1146, Bacteria |
HOGENOMi | CLU_042042_4_2_6 |
InParanoidi | P25889 |
PhylomeDBi | P25889 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11289-MONOMER |
SABIO-RKi | P25889 |
Miscellaneous databases
PROi | PR:P25889 |
Family and domain databases
Gene3Di | 3.20.20.70, 1 hit |
InterProi | View protein in InterPro IPR017896, 4Fe4S_Fe-S-bd IPR017900, 4Fe4S_Fe_S_CS IPR013785, Aldolase_TIM IPR005720, Dihydroorotate_DH IPR044512, DPYD |
PANTHERi | PTHR43073, PTHR43073, 2 hits |
Pfami | View protein in Pfam PF01180, DHO_dh, 1 hit |
TIGRFAMsi | TIGR01037, pyrD_sub1_fam, 1 hit |
PROSITEi | View protein in PROSITE PS00198, 4FE4S_FER_1, 1 hit PS51379, 4FE4S_FER_2, 2 hits |
MobiDBi | Search... |
Entry informationi
Entry namei | PREA_ECOLI | |
Accessioni | P25889Primary (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: | February 23, 2022 | |
This is version 167 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Direct protein sequencing, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families