ID NTRC_ECOLI Reviewed; 469 AA.
AC P0AFB8; P06713; Q2M8G5;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 27-MAR-2024, entry version 144.
DE RecName: Full=DNA-binding transcriptional regulator NtrC {ECO:0000305};
DE AltName: Full=Nitrogen regulation protein NR(I) {ECO:0000305};
DE AltName: Full=Nitrogen regulator I {ECO:0000303|PubMed:2574599};
DE Short=NRI {ECO:0000303|PubMed:2574599};
GN Name=glnG {ECO:0000303|PubMed:2882477};
GN Synonyms=glnT, ntrC {ECO:0000303|PubMed:2882477};
GN OrderedLocusNames=b3868, JW3839;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2882477; DOI=10.1093/nar/15.6.2757;
RA Miranda-Rios J., Sanchez-Pescador R., Urdea M., Covarrubias A.A.;
RT "The complete nucleotide sequence of the glnALG operon of Escherichia coli
RT K12.";
RL Nucleic Acids Res. 15:2757-2770(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8346018; DOI=10.1093/nar/21.15.3391;
RA Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome. III. DNA sequence of the region
RT from 87.2 to 89.2 minutes.";
RL Nucleic Acids Res. 21:3391-3398(1993).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 401-469.
RC STRAIN=K12;
RA Wachi M., Hamano-Takaku F., Nagano K., Kobayashi M., Yukawa H., Nagai K.;
RL Submitted (SEP-1994) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=2874557; DOI=10.1073/pnas.83.16.5909;
RA Ninfa A.J., Magasanik B.;
RT "Covalent modification of the glnG product, NRI, by the glnL product, NRII,
RT regulates the transcription of the glnALG operon in Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 83:5909-5913(1986).
RN [7]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=3304660; DOI=10.1016/0092-8674(87)90170-x;
RA Ninfa A.J., Reitzer L.J., Magasanik B.;
RT "Initiation of transcription at the bacterial glnAp2 promoter by purified
RT E. coli components is facilitated by enhancers.";
RL Cell 50:1039-1046(1987).
RN [8]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=2574599; DOI=10.1016/0300-9084(89)90104-1;
RA Magasanik B.;
RT "Regulation of transcription of the glnALG operon of Escherichia coli by
RT protein phosphorylation.";
RL Biochimie 71:1005-1012(1989).
RN [9]
RP FUNCTION, SUBUNIT, AND PHOSPHORYLATION.
RX PubMed=1350679; DOI=10.1073/pnas.89.11.5088;
RA Weiss V., Claverie-Martin F., Magasanik B.;
RT "Phosphorylation of nitrogen regulator I of Escherichia coli induces strong
RT cooperative binding to DNA essential for activation of transcription.";
RL Proc. Natl. Acad. Sci. U.S.A. 89:5088-5092(1992).
RN [10]
RP FUNCTION.
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 [11]
RP SUBUNIT, AND DOMAIN.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15208307; DOI=10.1074/jbc.m405205200;
RA Yang X.F., Ji Y., Schneider B.L., Reitzer L.;
RT "Phosphorylation-independent dimer-dimer interactions by the enhancer-
RT binding activator NtrC of Escherichia coli: a third function for the C-
RT terminal domain.";
RL J. Biol. Chem. 279:36708-36714(2004).
CC -!- FUNCTION: Member of the two-component regulatory system NtrB/NtrC,
CC which controls expression of the nitrogen-regulated (ntr) genes in
CC response to nitrogen limitation. Phosphorylated NtrC binds directly to
CC DNA and stimulates the formation of open promoter-sigma54-RNA
CC polymerase complexes (PubMed:2874557, PubMed:3304660, PubMed:2574599,
CC PubMed:1350679). Activates transcription of many genes and operons
CC whose products minimize the slowing of growth under nitrogen-limiting
CC conditions, including genes coding for glutamine synthetase (glnA),
CC transporters, amino acid permeases and catabolic enzymes
CC (PubMed:11121068). {ECO:0000269|PubMed:11121068,
CC ECO:0000269|PubMed:1350679, ECO:0000269|PubMed:2574599,
CC ECO:0000269|PubMed:2874557, ECO:0000269|PubMed:3304660}.
CC -!- SUBUNIT: Homodimer. Phosphorylation of the N-terminal receiver domain
CC leads to the formation of oligomers (PubMed:1350679). Can also form
CC phosphorylation-independent oligomers (PubMed:15208307).
CC {ECO:0000269|PubMed:1350679, ECO:0000269|PubMed:15208307}.
CC -!- INTERACTION:
CC P0AFB8; P0ACZ4: evgA; NbExp=3; IntAct=EBI-1113197, EBI-548694;
CC P0AFB8; P0AFB5: glnL; NbExp=3; IntAct=EBI-1113197, EBI-701156;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: Contains an N-terminal receiver domain, a central output
CC domain, which hydrolyzes ATP, interacts with RNA polymerase and is
CC required for phosphorylation-dependent oligomerization, and a C-
CC terminal domain, which is involved in DNA binding, dimerization and
CC phosphorylation-independent oligomerization.
CC {ECO:0000305|PubMed:15208307}.
CC -!- PTM: Phosphorylated and dephosphorylated by NtrB (PubMed:2874557,
CC PubMed:2574599). Phosphorylation induces strong cooperative binding to
CC DNA (PubMed:1350679). {ECO:0000269|PubMed:1350679,
CC ECO:0000269|PubMed:2574599, ECO:0000269|PubMed:2874557}.
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DR EMBL; X05173; CAA28808.1; -; Genomic_DNA.
DR EMBL; L19201; AAB03002.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76865.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77441.1; -; Genomic_DNA.
DR EMBL; D16509; BAA03962.1; -; Genomic_DNA.
DR PIR; B30377; RGECGG.
DR RefSeq; NP_418304.1; NC_000913.3.
DR RefSeq; WP_001188777.1; NZ_SSZK01000026.1.
DR AlphaFoldDB; P0AFB8; -.
DR BMRB; P0AFB8; -.
DR SMR; P0AFB8; -.
DR BioGRID; 4262628; 171.
DR BioGRID; 852658; 2.
DR DIP; DIP-9781N; -.
DR IntAct; P0AFB8; 6.
DR STRING; 511145.b3868; -.
DR jPOST; P0AFB8; -.
DR PaxDb; 511145-b3868; -.
DR EnsemblBacteria; AAC76865; AAC76865; b3868.
DR GeneID; 75174103; -.
DR GeneID; 948361; -.
DR KEGG; ecj:JW3839; -.
DR KEGG; eco:b3868; -.
DR PATRIC; fig|1411691.4.peg.2843; -.
DR EchoBASE; EB0380; -.
DR eggNOG; COG2204; Bacteria.
DR HOGENOM; CLU_000445_0_1_6; -.
DR InParanoid; P0AFB8; -.
DR OMA; LENICHW; -.
DR OrthoDB; 9804019at2; -.
DR PhylomeDB; P0AFB8; -.
DR BioCyc; EcoCyc:PROTEIN-NRI; -.
DR PRO; PR:P0AFB8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0000156; F:phosphorelay response regulator activity; IEA:InterPro.
DR GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
DR GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR GO; GO:0006355; P:regulation of DNA-templated transcription; IEA:InterPro.
DR GO; GO:0006808; P:regulation of nitrogen utilization; IEA:InterPro.
DR CDD; cd00009; AAA; 1.
DR CDD; cd19919; REC_NtrC; 1.
DR Gene3D; 1.10.8.60; -; 1.
DR Gene3D; 3.40.50.2300; -; 1.
DR Gene3D; 1.10.10.60; Homeodomain-like; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011006; CheY-like_superfamily.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR002197; HTH_Fis.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
DR InterPro; IPR002078; Sigma_54_int.
DR InterPro; IPR025662; Sigma_54_int_dom_ATP-bd_1.
DR InterPro; IPR025943; Sigma_54_int_dom_ATP-bd_2.
DR InterPro; IPR025944; Sigma_54_int_dom_CS.
DR InterPro; IPR010114; Transcript_reg_NtrC.
DR NCBIfam; TIGR01818; ntrC; 1.
DR PANTHER; PTHR32071:SF15; DNA-BINDING TRANSCRIPTIONAL REGULATOR NTRC; 1.
DR PANTHER; PTHR32071; TRANSCRIPTIONAL REGULATORY PROTEIN; 1.
DR Pfam; PF02954; HTH_8; 1.
DR Pfam; PF00072; Response_reg; 1.
DR Pfam; PF00158; Sigma54_activat; 1.
DR PRINTS; PR01590; HTHFIS.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00448; REC; 1.
DR SUPFAM; SSF52172; CheY-like; 1.
DR SUPFAM; SSF46689; Homeodomain-like; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS50110; RESPONSE_REGULATORY; 1.
DR PROSITE; PS00675; SIGMA54_INTERACT_1; 1.
DR PROSITE; PS00676; SIGMA54_INTERACT_2; 1.
DR PROSITE; PS00688; SIGMA54_INTERACT_3; 1.
DR PROSITE; PS50045; SIGMA54_INTERACT_4; 1.
PE 1: Evidence at protein level;
KW Activator; ATP-binding; Cytoplasm; DNA-binding; Nitrogen fixation;
KW Nucleotide-binding; Phosphoprotein; Reference proteome; Repressor;
KW Transcription; Transcription regulation; Two-component regulatory system.
FT CHAIN 1..469
FT /note="DNA-binding transcriptional regulator NtrC"
FT /id="PRO_0000081165"
FT DOMAIN 5..119
FT /note="Response regulatory"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00169"
FT DOMAIN 140..369
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 445..464
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT BINDING 168..175
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 231..240
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT MOD_RES 54
FT /note="4-aspartylphosphate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00169"
FT CONFLICT 142..144
FT /note="GEA -> AK (in Ref. 1; CAA28808)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 469 AA; 52255 MW; 645F401D4A10EFA0 CRC64;
MQRGIVWVVD DDSSIRWVLE RALAGAGLTC TTFENGAEVL EALASKTPDV LLSDIRMPGM
DGLALLKQIK QRHPMLPVII MTAHSDLDAA VSAYQQGAFD YLPKPFDIDE AVALVERAIS
HYQEQQQPRN VQLNGPTTDI IGEAPAMQDV FRIIGRLSRS SISVLINGES GTGKELVAHA
LHRHSPRAKA PFIALNMAAI PKDLIESELF GHEKGAFTGA NTIRQGRFEQ ADGGTLFLDE
IGDMPLDVQT RLLRVLADGQ FYRVGGYAPV KVDVRIIAAT HQNLEQRVQE GKFREDLFHR
LNVIRVHLPP LRERREDIPR LARHFLQVAA RELGVEAKLL HPETEAALTR LAWPGNVRQL
ENTCRWLTVM AAGQEVLIQD LPGELFESTV AESTSQMQPD SWATLLAQWA DRALRSGHQN
LLSEAQPELE RTLLTTALRH TQGHKQEAAR LLGWGRNTLT RKLKELGME
//
