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Protein

Pyrimidine monooxygenase RutA

Gene

rutA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

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).

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

GO - Biological processi

  • nitrogen utilization Source: UniProtKB
  • pyrimidine nucleobase catabolic process Source: EcoCyc
  • thymine catabolic process Source: CACAO
  • uracil catabolic process Source: UniProtKB

Keywordsi

Molecular functionMonooxygenase, Oxidoreductase
LigandFlavoprotein, FMN, NADP

Enzyme and pathway databases

BioCyciEcoCyc:G6523-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, 23 interactors
IntActiP75898, 7 interactors
STRINGi316385.ECDH10B_1084

Structurei

Secondary structure

1382
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi21 – 25Combined sources5
Turni30 – 33Combined sources4
Helixi46 – 58Combined sources13
Beta strandi63 – 65Combined sources3
Turni75 – 81Combined sources7
Helixi86 – 95Combined sources10
Beta strandi98 – 107Combined sources10
Turni108 – 110Combined sources3
Helixi113 – 127Combined sources15
Beta strandi131 – 136Combined sources6
Helixi141 – 145Combined sources5
Turni146 – 148Combined sources3
Helixi155 – 176Combined sources22
Beta strandi177 – 179Combined sources3
Beta strandi189 – 192Combined sources4
Beta strandi202 – 205Combined sources4
Helixi210 – 219Combined sources10
Beta strandi221 – 226Combined sources6
Beta strandi229 – 231Combined sources3
Turni233 – 236Combined sources4
Helixi237 – 248Combined sources12
Turni249 – 251Combined sources3
Beta strandi255 – 267Combined sources13
Helixi268 – 280Combined sources13
Helixi284 – 290Combined sources7
Helixi315 – 317Combined sources3
Beta strandi322 – 326Combined sources5
Helixi327 – 338Combined sources12
Beta strandi343 – 352Combined sources10
Helixi353 – 363Combined sources11
Helixi365 – 367Combined sources3
Helixi369 – 371Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5WANX-ray1.80A2-382[»]
ProteinModelPortaliP75898
SMRiP75898
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
InterProiView protein in InterPro
IPR011251 Luciferase-like_dom
IPR036661 Luciferase-like_sf
IPR019914 Pyrimidine_monooxygenase_RutA
PfamiView protein in Pfam
PF00296 Bac_luciferase, 1 hit
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
WP_001326839.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74097; AAC74097; b1012
BAA35789; BAA35789; BAA35789
GeneIDi945643
KEGGiecj:JW0997
eco:b1012
PATRICifig|511145.12.peg.1050

Similar proteinsi

Entry informationi

Entry nameiRUTA_ECOLI
AccessioniPrimary (citable) accession number: P75898
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: December 4, 2007
Last modified: March 28, 2018
This is version 128 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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Main funding by: National Institutes of Health