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Protein

Pyrimidine monooxygenase RutA

Gene

rutA

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

Functioni

Catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid. It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduced to ureidoacrylate. Requires the flavin reductase RutF to regenerate FMN in vivo. RutF can be substituted by Fre in vitro.2 Publications

Catalytic activityi

Uracil + FMNH2 + O2 = (Z)-3-ureidoacrylate peracid + FMN + H2O.1 Publication
Thymine + FMNH2 + O2 = (Z)-2-methylureidoacrylate peracid + FMN + H2O.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei134FMNSequence analysis1
Binding sitei143FMNSequence analysis1
Binding sitei209FMNSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi68 – 69FMNSequence analysis2
Nucleotide bindingi159 – 160FMNSequence analysis2

GO - Molecular functioni

  • alkanesulfonate monooxygenase activity Source: GO_Central
  • monooxygenase activity Source: UniProtKB
  • uracil oxygenase activity Source: CACAO

GO - Biological processi

  • alkanesulfonate catabolic process Source: GO_Central
  • nitrogen utilization Source: UniProtKB
  • pyrimidine nucleobase catabolic process Source: EcoCyc
  • thymine catabolic process Source: CACAO
  • uracil catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Monooxygenase, Oxidoreductase

Keywords - Ligandi

Flavoprotein, FMN, NADP

Enzyme and pathway databases

BioCyciEcoCyc:G6523-MONOMER.
ECOL316407:JW0997-MONOMER.
MetaCyc:G6523-MONOMER.
BRENDAi1.14.99.46. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyrimidine monooxygenase RutA (EC:1.14.99.46)
Gene namesi
Name:rutA
Synonyms:ycdM
Ordered Locus Names:b1012, JW0997
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13859. rutA.

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene lose the ability to utilize pyrimidine nucleosides and bases as the sole source of nitrogen at room temperature.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001688021 – 382Pyrimidine monooxygenase RutAAdd BLAST382

Proteomic databases

PaxDbiP75898.
PRIDEiP75898.

Expressioni

Inductioni

Up-regulated by the nitrogen regulatory protein C (NtrC also called GlnG) and repressed by RutR.2 Publications

Interactioni

Protein-protein interaction databases

BioGridi4260038. 22 interactors.
IntActiP75898. 7 interactors.
STRINGi511145.b1012.

Structurei

3D structure databases

ProteinModelPortaliP75898.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105EQP. Bacteria.
COG2141. LUCA.
HOGENOMiHOG000268769.
InParanoidiP75898.
KOiK09018.
OMAiADYNFCF.
PhylomeDBiP75898.

Family and domain databases

Gene3Di3.20.20.30. 1 hit.
HAMAPiMF_01699. RutA. 1 hit.
InterProiIPR011251. Luciferase-like_dom.
IPR019914. Pyrimidine_monooxygenase_RutA.
[Graphical view]
PfamiPF00296. Bac_luciferase. 1 hit.
[Graphical view]
SUPFAMiSSF51679. SSF51679. 1 hit.
TIGRFAMsiTIGR03612. RutA. 1 hit.

Sequencei

Sequence statusi: Complete.

P75898-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQDAAPRLTF TLRDEERLMM KIGVFVPIGN NGWLISTHAP QYMPTFELNK
60 70 80 90 100
AIVQKAEHYH FDFALSMIKL RGFGGKTEFW DHNLESFTLM AGLAAVTSRI
110 120 130 140 150
QIYATAATLT LPPAIVARMA ATIDSISGGR FGVNLVTGWQ KPEYEQMGIW
160 170 180 190 200
PGDDYFSRRY DYLTEYVQVL RDLWGTGKSD FKGDFFTMND CRVSPQPSVP
210 220 230 240 250
MKVICAGQSD AGMAFSARYA DFNFCFGKGV NTPTAFAPTA ARMKQAAEQT
260 270 280 290 300
GRDVGSYVLF MVIADETDDA ARAKWEHYKA GADEEALSWL TEQSQKDTRS
310 320 330 340 350
GTDTNVRQMA DPTSAVNINM GTLVGSYASV ARMLDEVASV PGAEGVLLTF
360 370 380
DDFLSGIETF GERIQPLMQC RAHLPALTQE VA
Length:382
Mass (Da):42,219
Last modified:December 4, 2007 - v3
Checksum:i705312739DFA1A9D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74097.1.
AP009048 Genomic DNA. Translation: BAA35789.1.
PIRiB64843.
RefSeqiNP_415532.3. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC74097; AAC74097; b1012.
BAA35789; BAA35789; BAA35789.
GeneIDi945643.
KEGGiecj:JW0997.
eco:b1012.
PATRICi32117253. VBIEscCol129921_1050.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74097.1.
AP009048 Genomic DNA. Translation: BAA35789.1.
PIRiB64843.
RefSeqiNP_415532.3. NC_000913.3.

3D structure databases

ProteinModelPortaliP75898.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260038. 22 interactors.
IntActiP75898. 7 interactors.
STRINGi511145.b1012.

Proteomic databases

PaxDbiP75898.
PRIDEiP75898.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74097; AAC74097; b1012.
BAA35789; BAA35789; BAA35789.
GeneIDi945643.
KEGGiecj:JW0997.
eco:b1012.
PATRICi32117253. VBIEscCol129921_1050.

Organism-specific databases

EchoBASEiEB3619.
EcoGeneiEG13859. rutA.

Phylogenomic databases

eggNOGiENOG4105EQP. Bacteria.
COG2141. LUCA.
HOGENOMiHOG000268769.
InParanoidiP75898.
KOiK09018.
OMAiADYNFCF.
PhylomeDBiP75898.

Enzyme and pathway databases

BioCyciEcoCyc:G6523-MONOMER.
ECOL316407:JW0997-MONOMER.
MetaCyc:G6523-MONOMER.
BRENDAi1.14.99.46. 2026.

Miscellaneous databases

PROiP75898.

Family and domain databases

Gene3Di3.20.20.30. 1 hit.
HAMAPiMF_01699. RutA. 1 hit.
InterProiIPR011251. Luciferase-like_dom.
IPR019914. Pyrimidine_monooxygenase_RutA.
[Graphical view]
PfamiPF00296. Bac_luciferase. 1 hit.
[Graphical view]
SUPFAMiSSF51679. SSF51679. 1 hit.
TIGRFAMsiTIGR03612. RutA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRUTA_ECOLI
AccessioniPrimary (citable) accession number: P75898
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: December 4, 2007
Last modified: November 2, 2016
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The Rut pathway degrades exogenous pyrimidines as the sole nitrogen source at room temperature but not at 37 degrees Celsius, a restriction that is apparently a consequence of an inadequate ability to remove toxic malonic semialdehyde at the higher temperature (RutE/YdfG function).

Keywords - Technical termi

Complete proteome, 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.