NAGR_BACSU
ID NAGR_BACSU Reviewed; 243 AA.
AC O34817; Q795E9;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=HTH-type transcriptional repressor NagR {ECO:0000305};
DE AltName: Full=N-acetylglucosamine utilization regulator {ECO:0000303|PubMed:21602348};
GN Name=nagR {ECO:0000303|PubMed:21602348}; Synonyms=yvoA {ECO:0000303|Ref.1};
GN OrderedLocusNames=BSU35030;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Lazarevic V., Soldo B., Rivolta C., Reynolds S., Mauel C., Karamata D.;
RT "Nucleotide sequence of the 300-304 chromosomal segment of Bacillus
RT subtilis.";
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16207374; DOI=10.1186/1471-2180-5-57;
RA You C., Lu H., Sekowska A., Fang G., Wang Y., Gilles A.-M., Danchin A.;
RT "The two authentic methionine aminopeptidase genes are differentially
RT expressed in Bacillus subtilis.";
RL BMC Microbiol. 5:57-57(2005).
RN [4]
RP SUBUNIT, AND CRYSTALLIZATION.
RC STRAIN=168;
RX PubMed=19342794; DOI=10.1107/s1744309109008628;
RA Resch M., Roth H.M., Kottmair M., Sevvana M., Bertram R., Titgemeyer F.,
RA Muller Y.A.;
RT "Cloning, expression, purification, crystallization and preliminary X-ray
RT diffraction analysis of YvoA from Bacillus subtilis.";
RL Acta Crystallogr. F 65:410-414(2009).
RN [5]
RP FUNCTION, DNA-BINDING, ACTIVITY REGULATION, AND DISRUPTION PHENOTYPE.
RX PubMed=21602348; DOI=10.1128/jb.00264-11;
RA Bertram R., Rigali S., Wood N., Lulko A.T., Kuipers O.P., Titgemeyer F.;
RT "Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus
RT subtilis.";
RL J. Bacteriol. 193:3525-3536(2011).
RN [6]
RP FUNCTION, DNA-BINDING, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=24673833; DOI=10.1111/mmi.12544;
RA Gaugue I., Oberto J., Plumbridge J.;
RT "Regulation of amino sugar utilization in Bacillus subtilis by the GntR
RT family regulators, NagR and GamR.";
RL Mol. Microbiol. 92:100-115(2014).
RN [7] {ECO:0007744|PDB:2WV0}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS), FUNCTION, DNA-BINDING, ACTIVITY
RP REGULATION, SUBUNIT, DOMAIN, AND MUTAGENESIS OF ILE-209; GLU-222 AND
RP ALA-224.
RX PubMed=20047956; DOI=10.1093/nar/gkp1191;
RA Resch M., Schiltz E., Titgemeyer F., Muller Y.A.;
RT "Insight into the induction mechanism of the GntR/HutC bacterial
RT transcription regulator YvoA.";
RL Nucleic Acids Res. 38:2485-2497(2010).
RN [8] {ECO:0007744|PDB:4U0V, ECO:0007744|PDB:4U0W, ECO:0007744|PDB:4U0Y, ECO:0007744|PDB:4WWC}
RP X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) IN COMPLEXES WITH PUTATIVE EFFECTORS
RP GLCN6P AND GLCNAC6P AND DNA, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=25564531; DOI=10.1093/nar/gku1374;
RA Fillenberg S.B., Grau F.C., Seidel G., Muller Y.A.;
RT "Structural insight into operator dre-sites recognition and effector
RT binding in the GntR/HutC transcription regulator NagR.";
RL Nucleic Acids Res. 43:1283-1296(2015).
CC -!- FUNCTION: Main transcriptional repressor of genes involved in N-
CC acetylglucosamine (GlcNAc) transport and utilization (PubMed:21602348,
CC PubMed:20047956, PubMed:24673833). Represses the expression of the
CC nagAB and nagP operons by binding directly within their upstream
CC regions (PubMed:21602348, PubMed:24673833). Binds to the DNA consensus
CC sequence 5'-ATTGGTATAGACAACT-3' (PubMed:21602348). Also acts as a weak
CC repressor of mapB expression (PubMed:16207374).
CC {ECO:0000269|PubMed:16207374, ECO:0000269|PubMed:20047956,
CC ECO:0000269|PubMed:21602348, ECO:0000269|PubMed:24673833}.
CC -!- ACTIVITY REGULATION: Binding to DNA is allosterically inhibited by an
CC effector molecule (PubMed:20047956, PubMed:21602348, PubMed:24673833,
CC PubMed:25564531). Binding of the effector to the C-terminal domain
CC leads to a conformational change that modulates binding to DNA and
CC thereby regulates transcription of the target genes (PubMed:20047956,
CC PubMed:25564531). Glucosamine-6-phosphate (GlcN6P) and/or N-
CC acetylglucosamine-6-phosphate (GlcNAc6P) are putative effectors of NagR
CC (PubMed:20047956, PubMed:21602348, PubMed:24673833, PubMed:25564531).
CC Binding of GlcNAc6P may prevent the protein-protein interactions
CC responsible for polymerization along the DNA, but not the specific DNA
CC binding (PubMed:24673833). {ECO:0000269|PubMed:20047956,
CC ECO:0000269|PubMed:21602348, ECO:0000269|PubMed:24673833,
CC ECO:0000269|PubMed:25564531}.
CC -!- SUBUNIT: Homodimer (PubMed:19342794, PubMed:20047956, PubMed:25564531).
CC Forms dimers via the C-terminal effector-binding domain
CC (PubMed:20047956). At high concentrations, probably forms polymers
CC along the DNA (PubMed:24673833). {ECO:0000269|PubMed:19342794,
CC ECO:0000269|PubMed:20047956, ECO:0000269|PubMed:24673833,
CC ECO:0000269|PubMed:25564531}.
CC -!- DOMAIN: The N-terminal region contains a canonical wHTH DNA-binding
CC domain. It is linked via a 21 residue-long linker to the C-terminal
CC domain, which binds the effector molecule.
CC {ECO:0000269|PubMed:20047956}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene results in the modulation of
CC the expression of many important genes, probably indirectly due to an
CC excess of the crucial molecules acetate, ammonia, and fructose-6-
CC phosphate, resulting from complete hydrolysis of GlcNAc
CC (PubMed:21602348). Disruption of the gene induces a slight but
CC consistent increase in MapB activity (PubMed:16207374).
CC {ECO:0000269|PubMed:16207374, ECO:0000269|PubMed:21602348}.
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DR EMBL; AF017113; AAC67283.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15508.1; -; Genomic_DNA.
DR PIR; D70044; D70044.
DR RefSeq; NP_391383.1; NC_000964.3.
DR RefSeq; WP_003228089.1; NZ_JNCM01000033.1.
DR PDB; 2WV0; X-ray; 2.40 A; A/B/C/D/E/F/G/H/I/J=1-243.
DR PDB; 4U0V; X-ray; 2.05 A; A/B=1-243.
DR PDB; 4U0W; X-ray; 2.00 A; A/B=1-243.
DR PDB; 4U0Y; X-ray; 1.91 A; A/B/C/D=1-75.
DR PDB; 4WWC; X-ray; 2.90 A; A/B=1-243.
DR PDBsum; 2WV0; -.
DR PDBsum; 4U0V; -.
DR PDBsum; 4U0W; -.
DR PDBsum; 4U0Y; -.
DR PDBsum; 4WWC; -.
DR AlphaFoldDB; O34817; -.
DR SMR; O34817; -.
DR STRING; 224308.BSU35030; -.
DR PaxDb; O34817; -.
DR PRIDE; O34817; -.
DR EnsemblBacteria; CAB15508; CAB15508; BSU_35030.
DR GeneID; 936626; -.
DR KEGG; bsu:BSU35030; -.
DR PATRIC; fig|224308.179.peg.3791; -.
DR eggNOG; COG2188; Bacteria.
DR InParanoid; O34817; -.
DR OMA; LDMREGQ; -.
DR PhylomeDB; O34817; -.
DR BioCyc; BSUB:BSU35030-MON; -.
DR EvolutionaryTrace; O34817; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR CDD; cd07377; WHTH_GntR; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.40.1410.10; -; 1.
DR InterPro; IPR028978; Chorismate_lyase_/UTRA_dom_sf.
DR InterPro; IPR000524; Tscrpt_reg_HTH_GntR.
DR InterPro; IPR011663; UTRA.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF00392; GntR; 1.
DR Pfam; PF07702; UTRA; 1.
DR PRINTS; PR00035; HTHGNTR.
DR SMART; SM00345; HTH_GNTR; 1.
DR SMART; SM00866; UTRA; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR SUPFAM; SSF64288; SSF64288; 1.
DR PROSITE; PS50949; HTH_GNTR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..243
FT /note="HTH-type transcriptional repressor NagR"
FT /id="PRO_0000360728"
FT DOMAIN 9..77
FT /note="HTH gntR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00307"
FT DNA_BIND 37..56
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00307"
FT BINDING 89..90
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0000305|PubMed:20047956, ECO:0007744|PDB:4U0V"
FT BINDING 89..90
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT BINDING 133..135
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0000305|PubMed:20047956, ECO:0007744|PDB:4U0V"
FT BINDING 133..135
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT BINDING 145
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0V"
FT BINDING 145
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT BINDING 165..167
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0000305|PubMed:20047956, ECO:0007744|PDB:4U0V"
FT BINDING 165..167
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT BINDING 222
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0V"
FT BINDING 222
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT BINDING 228
FT /ligand="alpha-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:75989"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0V"
FT BINDING 228
FT /ligand="N-acetyl-D-glucosamine 6-phosphate"
FT /ligand_id="ChEBI:CHEBI:57513"
FT /ligand_note="putative effector"
FT /evidence="ECO:0000269|PubMed:25564531,
FT ECO:0007744|PDB:4U0W"
FT MUTAGEN 209
FT /note="I->E: Abolishes GlcNAc6P binding."
FT /evidence="ECO:0000269|PubMed:20047956"
FT MUTAGEN 209
FT /note="I->L: No or little effects on GlcNAc6P binding."
FT /evidence="ECO:0000269|PubMed:20047956"
FT MUTAGEN 222
FT /note="E->D: No or little effects on GlcNAc6P binding."
FT /evidence="ECO:0000269|PubMed:20047956"
FT MUTAGEN 224
FT /note="A->R: Abolishes GlcNAc6P binding."
FT /evidence="ECO:0000269|PubMed:20047956"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:4U0Y"
FT HELIX 11..24
FT /evidence="ECO:0007829|PDB:4U0Y"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:4U0V"
FT HELIX 37..44
FT /evidence="ECO:0007829|PDB:4U0Y"
FT HELIX 48..60
FT /evidence="ECO:0007829|PDB:4U0Y"
FT STRAND 63..67
FT /evidence="ECO:0007829|PDB:4U0Y"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:4U0Y"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:4U0Y"
FT STRAND 79..82
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 89..95
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 100..111
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 114..120
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 127..137
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 140..150
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 159..162
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 166..174
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 178..189
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 192..198
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 205..215
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 220..229
FT /evidence="ECO:0007829|PDB:4U0W"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:4U0W"
FT STRAND 233..240
FT /evidence="ECO:0007829|PDB:4U0W"
SQ SEQUENCE 243 AA; 27507 MW; 7E8B79E48EA863B7 CRC64;
MNINKQSPIP IYYQIMEQLK TQIKNGELQP DMPLPSEREY AEQFGISRMT VRQALSNLVN
EGLLYRLKGR GTFVSKPKME QALQGLTSFT EDMKSRGMTP GSRLIDYQLI DSTEELAAIL
GCGHPSSIHK ITRVRLANDI PMAIESSHIP FELAGELNES HFQSSIYDHI ERYNSIPISR
AKQELEPSAA TTEEANILGI QKGAPVLLIK RTTYLQNGTA FEHAKSVYRG DRYTFVHYMD
RLS
