RUTA_ECOLI
ID RUTA_ECOLI Reviewed; 382 AA.
AC P75898;
DT 27-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 3.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Pyrimidine monooxygenase RutA;
DE EC=1.14.99.46 {ECO:0000269|PubMed:20369853, ECO:0000269|PubMed:28661684};
GN Name=rutA; Synonyms=ycdM; OrderedLocusNames=b1012, JW0997;
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 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
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 [3]
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 [4]
RP INDUCTION.
RX PubMed=11121068; DOI=10.1073/pnas.97.26.14674;
RA Zimmer D.P., Soupene E., Lee H.L., Wendisch V.F., Khodursky A.B.,
RA Peter B.J., Bender R.A., Kustu S.;
RT "Nitrogen regulatory protein C-controlled genes of Escherichia coli:
RT scavenging as a defense against nitrogen limitation.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:14674-14679(2000).
RN [5]
RP FUNCTION IN PYRIMIDINE CATABOLISM, SUBSTRATE SPECIFICITY, DISRUPTION
RP PHENOTYPE, AND NOMENCLATURE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16540542; DOI=10.1073/pnas.0600521103;
RA Loh K.D., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim K.-S.,
RA Parales R., Zhou Z., Inwood W., Kustu S.;
RT "A previously undescribed pathway for pyrimidine catabolism.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:5114-5119(2006).
RN [6]
RP INDUCTION.
RX PubMed=17919280; DOI=10.1111/j.1365-2958.2007.05954.x;
RA Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A.;
RT "RutR is the uracil/thymine-sensing master regulator of a set of genes for
RT synthesis and degradation of pyrimidines.";
RL Mol. Microbiol. 66:744-757(2007).
RN [7]
RP FUNCTION AS A PYRIMIDINE OXYGENASE.
RX PubMed=20400551; DOI=10.1128/jb.00201-10;
RA Kim K.S., Pelton J.G., Inwood W.B., Andersen U., Kustu S., Wemmer D.E.;
RT "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity
RT problems.";
RL J. Bacteriol. 192:4089-4102(2010).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RX PubMed=28661684; DOI=10.1021/acs.biochem.7b00493;
RA Adak S., Begley T.P.;
RT "RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation
RT of a Flavin-N5-oxide.";
RL Biochemistry 56:3708-3709(2017).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH FMN, AND CATALYTIC
RP ACTIVITY.
RX PubMed=20369853; DOI=10.1021/ja9107676;
RA Mukherjee T., Zhang Y., Abdelwahed S., Ealick S.E., Begley T.P.;
RT "Catalysis of a flavoenzyme-mediated amide hydrolysis.";
RL J. Am. Chem. Soc. 132:5550-5551(2010).
CC -!- FUNCTION: Catalyzes the pyrimidine ring opening between N-3 and C-4 by
CC an unusual flavin hydroperoxide-catalyzed mechanism, adding oxygen
CC atoms in the process to yield ureidoacrylate peracid, that immediately
CC reacts with FMN forming ureidoacrylate and FMN-N(5)-oxide. The FMN-
CC N(5)-oxide reacts spontaneously with NADH to produce FMN. Requires the
CC flavin reductase RutF to regenerate FMN in vivo. RutF can be
CC substituted by Fre in vitro. {ECO:0000269|PubMed:16540542,
CC ECO:0000269|PubMed:20400551, ECO:0000269|PubMed:28661684}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=FMNH2 + NADH + O2 + uracil = (Z)-3-ureidoacrylate + FMN + H(+)
CC + H2O + NAD(+); Xref=Rhea:RHEA:31587, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:17568,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57618, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58210, ChEBI:CHEBI:59891; EC=1.14.99.46;
CC Evidence={ECO:0000269|PubMed:20369853, ECO:0000269|PubMed:28661684};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=FMNH2 + NADH + O2 + thymine = (Z)-2-methylureidoacrylate + FMN
CC + H(+) + H2O + NAD(+); Xref=Rhea:RHEA:31599, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:17821,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57618, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58210, ChEBI:CHEBI:143783; EC=1.14.99.46;
CC Evidence={ECO:0000269|PubMed:20369853, ECO:0000269|PubMed:28661684};
CC -!- INDUCTION: Up-regulated by the nitrogen regulatory protein C (NtrC also
CC called GlnG) and repressed by RutR. {ECO:0000269|PubMed:11121068,
CC ECO:0000269|PubMed:17919280}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lose the ability to
CC utilize pyrimidine nucleosides and bases as the sole source of nitrogen
CC at room temperature. {ECO:0000269|PubMed:16540542}.
CC -!- MISCELLANEOUS: The Rut pathway degrades exogenous pyrimidines as the
CC sole nitrogen source at room temperature but not at 37 degrees Celsius,
CC a restriction that is apparently a consequence of an inadequate ability
CC to remove toxic malonic semialdehyde at the higher temperature
CC (RutE/YdfG function).
CC -!- SIMILARITY: Belongs to the NtaA/SnaA/DszA monooxygenase family. RutA
CC subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U00096; AAC74097.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35789.1; -; Genomic_DNA.
DR PIR; B64843; B64843.
DR RefSeq; NP_415532.3; NC_000913.3.
DR PDB; 5WAN; X-ray; 1.80 A; A=2-382.
DR PDB; 6SGG; X-ray; 1.80 A; AAA=20-382.
DR PDB; 6SGL; X-ray; 2.01 A; AAA=19-382.
DR PDB; 6SGM; X-ray; 2.00 A; AAA=20-382.
DR PDB; 6SGN; X-ray; 2.50 A; AAA=20-382.
DR PDB; 6TEE; X-ray; 2.20 A; AAA=20-382.
DR PDB; 6TEF; X-ray; 1.80 A; AAA=19-382.
DR PDB; 6TEG; X-ray; 1.80 A; AAA=19-382.
DR PDBsum; 5WAN; -.
DR PDBsum; 6SGG; -.
DR PDBsum; 6SGL; -.
DR PDBsum; 6SGM; -.
DR PDBsum; 6SGN; -.
DR PDBsum; 6TEE; -.
DR PDBsum; 6TEF; -.
DR PDBsum; 6TEG; -.
DR AlphaFoldDB; P75898; -.
DR SMR; P75898; -.
DR BioGRID; 4260038; 23.
DR IntAct; P75898; 7.
DR STRING; 511145.b1012; -.
DR PaxDb; P75898; -.
DR PRIDE; P75898; -.
DR EnsemblBacteria; AAC74097; AAC74097; b1012.
DR EnsemblBacteria; BAA35789; BAA35789; BAA35789.
DR GeneID; 945643; -.
DR KEGG; ecj:JW0997; -.
DR KEGG; eco:b1012; -.
DR PATRIC; fig|511145.12.peg.1050; -.
DR EchoBASE; EB3619; -.
DR eggNOG; COG2141; Bacteria.
DR HOGENOM; CLU_027853_1_1_6; -.
DR InParanoid; P75898; -.
DR OMA; ADYNFCF; -.
DR PhylomeDB; P75898; -.
DR BioCyc; EcoCyc:G6523-MON; -.
DR BioCyc; MetaCyc:G6523-MON; -.
DR BRENDA; 1.14.99.46; 2026.
DR PRO; PR:P75898; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008726; F:alkanesulfonate monooxygenase activity; IBA:GO_Central.
DR GO; GO:0004497; F:monooxygenase activity; IDA:UniProtKB.
DR GO; GO:0052614; F:uracil oxygenase activity; IDA:EcoCyc.
DR GO; GO:0046306; P:alkanesulfonate catabolic process; IBA:GO_Central.
DR GO; GO:0019740; P:nitrogen utilization; IDA:UniProtKB.
DR GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IMP:EcoCyc.
DR GO; GO:0006210; P:thymine catabolic process; IDA:CACAO.
DR GO; GO:0006212; P:uracil catabolic process; IDA:UniProtKB.
DR Gene3D; 3.20.20.30; -; 1.
DR HAMAP; MF_01699; RutA; 1.
DR InterPro; IPR011251; Luciferase-like_dom.
DR InterPro; IPR036661; Luciferase-like_sf.
DR InterPro; IPR019914; Pyrimidine_monooxygenase_RutA.
DR Pfam; PF00296; Bac_luciferase; 1.
DR SUPFAM; SSF51679; SSF51679; 1.
DR TIGRFAMs; TIGR03612; RutA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; Monooxygenase; NADP; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..382
FT /note="Pyrimidine monooxygenase RutA"
FT /id="PRO_0000168802"
FT BINDING 68..69
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255"
FT BINDING 134
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255"
FT BINDING 143
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255"
FT BINDING 159..160
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255"
FT BINDING 209
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255"
FT STRAND 21..25
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 30..33
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 46..58
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 75..81
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 86..95
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 98..107
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 113..127
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 141..145
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 146..148
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 155..176
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 210..219
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 221..226
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 233..236
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 237..248
FT /evidence="ECO:0007829|PDB:5WAN"
FT TURN 249..251
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 255..267
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 268..280
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 284..290
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 322..326
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 327..338
FT /evidence="ECO:0007829|PDB:5WAN"
FT STRAND 343..352
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 353..363
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 365..367
FT /evidence="ECO:0007829|PDB:5WAN"
FT HELIX 369..371
FT /evidence="ECO:0007829|PDB:5WAN"
SQ SEQUENCE 382 AA; 42219 MW; 705312739DFA1A9D CRC64;
MQDAAPRLTF TLRDEERLMM KIGVFVPIGN NGWLISTHAP QYMPTFELNK AIVQKAEHYH
FDFALSMIKL RGFGGKTEFW DHNLESFTLM AGLAAVTSRI QIYATAATLT LPPAIVARMA
ATIDSISGGR FGVNLVTGWQ KPEYEQMGIW PGDDYFSRRY DYLTEYVQVL RDLWGTGKSD
FKGDFFTMND CRVSPQPSVP MKVICAGQSD AGMAFSARYA DFNFCFGKGV NTPTAFAPTA
ARMKQAAEQT GRDVGSYVLF MVIADETDDA ARAKWEHYKA GADEEALSWL TEQSQKDTRS
GTDTNVRQMA DPTSAVNINM GTLVGSYASV ARMLDEVASV PGAEGVLLTF DDFLSGIETF
GERIQPLMQC RAHLPALTQE VA
