RUTR_ECOLI
ID RUTR_ECOLI Reviewed; 212 AA.
AC P0ACU2; P75899;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=HTH-type transcriptional regulator RutR;
DE AltName: Full=Rut operon repressor;
GN Name=rutR; Synonyms=ycdC; OrderedLocusNames=b1013, JW0998;
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 FUNCTION IN PYRIMIDINE CATABOLISM, 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 [5]
RP FUNCTION AS A TRANSCRIPTIONAL REGULATOR.
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 [6]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), AND SUBUNIT.
RG New York structural genomics research consortium (NYSGRC);
RT "Crystal structure of hypothetical transcriptional regulator ycdC from
RT Escherichia coli.";
RL Submitted (MAY-2003) to the PDB data bank.
CC -!- FUNCTION: Master transcription regulator which represses the
CC degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for
CC maintenance of metabolic balance between pyrimidines and purines. It
CC also regulates the synthesis of pyrimidine nucleotides and arginine
CC from glutamine (carAB) and the supply of glutamate (gadABWX).
CC {ECO:0000269|PubMed:16540542, ECO:0000269|PubMed:17919280}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.6}.
CC -!- INTERACTION:
CC P0ACU2; P04951: kdsB; NbExp=2; IntAct=EBI-1121539, EBI-544810;
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).
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DR EMBL; U00096; AAC74098.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35790.1; -; Genomic_DNA.
DR PIR; C64843; C64843.
DR RefSeq; NP_415533.1; NC_000913.3.
DR RefSeq; WP_000191701.1; NZ_SSZK01000002.1.
DR PDB; 3LOC; X-ray; 2.50 A; A/B/C/D=1-212.
DR PDB; 4JYK; X-ray; 1.70 A; A/B=1-212.
DR PDB; 4X1E; X-ray; 2.40 A; A/B=1-212.
DR PDB; 4XK4; X-ray; 2.27 A; A/B/C/D=1-212.
DR PDBsum; 3LOC; -.
DR PDBsum; 4JYK; -.
DR PDBsum; 4X1E; -.
DR PDBsum; 4XK4; -.
DR AlphaFoldDB; P0ACU2; -.
DR SMR; P0ACU2; -.
DR BioGRID; 849464; 5.
DR IntAct; P0ACU2; 23.
DR STRING; 511145.b1013; -.
DR jPOST; P0ACU2; -.
DR PaxDb; P0ACU2; -.
DR PRIDE; P0ACU2; -.
DR DNASU; 945075; -.
DR EnsemblBacteria; AAC74098; AAC74098; b1013.
DR EnsemblBacteria; BAA35790; BAA35790; BAA35790.
DR GeneID; 60667996; -.
DR GeneID; 66670709; -.
DR GeneID; 945075; -.
DR KEGG; ecj:JW0998; -.
DR KEGG; eco:b1013; -.
DR PATRIC; fig|1411691.4.peg.1258; -.
DR EchoBASE; EB2207; -.
DR eggNOG; COG1309; Bacteria.
DR HOGENOM; CLU_069356_1_0_6; -.
DR InParanoid; P0ACU2; -.
DR OMA; DPHHLIF; -.
DR PhylomeDB; P0ACU2; -.
DR BioCyc; EcoCyc:PD01352; -.
DR PRO; PR:P0ACU2; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR CollecTF; EXPREG_00000870; -.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:EcoCyc.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IBA:GO_Central.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR001647; HTH_TetR.
DR InterPro; IPR036271; Tet_transcr_reg_TetR-rel_C_sf.
DR InterPro; IPR019915; Tscrpt_reg_pyr_util_RutR.
DR InterPro; IPR013573; Tscrpt_reg_YcdC_C.
DR Pfam; PF08362; TetR_C_3; 1.
DR Pfam; PF00440; TetR_N; 1.
DR PRINTS; PR00455; HTHTETR.
DR SUPFAM; SSF46689; SSF46689; 1.
DR SUPFAM; SSF48498; SSF48498; 1.
DR TIGRFAMs; TIGR03613; RutR; 1.
DR PROSITE; PS50977; HTH_TETR_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..212
FT /note="HTH-type transcriptional regulator RutR"
FT /id="PRO_0000070635"
FT DOMAIN 17..77
FT /note="HTH tetR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00335"
FT DNA_BIND 39..58
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00335"
FT HELIX 14..34
FT /evidence="ECO:0007829|PDB:4JYK"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 41..48
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 52..58
FT /evidence="ECO:0007829|PDB:4JYK"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:3LOC"
FT HELIX 62..82
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 90..107
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 109..120
FT /evidence="ECO:0007829|PDB:4JYK"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 127..131
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 133..150
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 159..175
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:4JYK"
FT HELIX 191..209
FT /evidence="ECO:0007829|PDB:4JYK"
SQ SEQUENCE 212 AA; 23688 MW; E2459B85DFAC277A CRC64;
MTQGAVKTTG KRSRAVSAKK KAILSAALDT FSQFGFHGTR LEQIAELAGV SKTNLLYYFP
SKEALYIAVL RQILDIWLAP LKAFREDFAP LAAIKEYIRL KLEVSRDYPQ ASRLFCMEML
AGAPLLMDEL TGDLKALIDE KSALIAGWVK SGKLAPIDPQ HLIFMIWAST QHYADFAPQV
EAVTGATLRD EVFFNQTVEN VQRIIIEGIR PR
