DGOR_ECOLI
ID DGOR_ECOLI Reviewed; 229 AA.
AC P31460; O32529; P76735; Q2M807; Q6BF15;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 4.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Galactonate operon transcriptional repressor {ECO:0000305};
DE AltName: Full=HTH-type transcriptional repressor DgoR {ECO:0000305};
GN Name=dgoR {ECO:0000303|PubMed:211976}; Synonyms=yidW;
GN OrderedLocusNames=b4479, JW5627;
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 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
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 SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
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 FUNCTION, AND OPERON.
RC STRAIN=K12;
RX PubMed=211976; DOI=10.1007/bf00415730;
RA Cooper R.A.;
RT "The utilisation of D-galactonate and D-2-oxo-3-deoxygalactonate by
RT Escherichia coli K-12. Biochemical and genetical studies.";
RL Arch. Microbiol. 118:199-206(1978).
RN [6]
RP FUNCTION, DNA-BINDING, ACTIVITY REGULATION, INDUCTION, OPERON, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF ASP-7; LEU-34; THR-40; ARG-42; ARG-46 AND
RP SER-51.
RX PubMed=30455279; DOI=10.1128/jb.00281-18;
RA Singh B., Arya G., Kundu N., Sangwan A., Nongthombam S., Chaba R.;
RT "Molecular and functional insights into the regulation of D-galactonate
RT metabolism by the transcriptional regulator DgoR in Escherichia coli.";
RL J. Bacteriol. 201:e00281-e00281(2019).
RN [7]
RP FUNCTION, ACTIVITY REGULATION, SUBUNIT, DOMAIN, AND MUTAGENESIS OF ARG-102;
RP GLU-106; ASP-146; HIS-150; THR-191; LEU-192; HIS-195 AND SER-221.
RX PubMed=33068046; DOI=10.1111/mmi.14625;
RA Arya G., Pal M., Sharma M., Singh B., Singh S., Agrawal V., Chaba R.;
RT "Molecular insights into effector binding by DgoR, a GntR/FadR family
RT transcriptional repressor of D-galactonate metabolism in Escherichia
RT coli.";
RL Mol. Microbiol. 115:591-609(2021).
RN [8] {ECO:0007744|PDB:7C7E}
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH ZINC, FUNCTION,
RP ACTIVITY REGULATION, DOMAIN, AND MUTAGENESIS OF ARG-102; ASP-146; HIS-150;
RP GLN-173; ARG-179; TRP-181; ASP-184; THR-191; HIS-195; SER-221 AND ARG-224.
RX PubMed=33224125; DOI=10.3389/fmicb.2020.590330;
RA Lin Z., Sun Y., Liu Y., Tong S., Shang Z., Cai Y., Lin W.;
RT "Structural and functional analyses of the transcription repressor DgoR
RT from Escherichia coli reveal a divalent metal-containing D-galactonate
RT binding pocket.";
RL Front. Microbiol. 11:590330-590330(2020).
CC -!- FUNCTION: Involved in the regulation of D-galactonate metabolism
CC (PubMed:211976, PubMed:30455279). Represses the expression of the
CC dgoRKADT operon by binding to two closely spaced inverted repeats in
CC the cis-acting element, which overlap with the D-galactonate responsive
CC dgo promoter (PubMed:30455279). Employs a derepression mechanism using
CC D-galactonate as a specific effector molecule (PubMed:30455279,
CC PubMed:33224125, PubMed:33068046). {ECO:0000269|PubMed:211976,
CC ECO:0000269|PubMed:30455279, ECO:0000269|PubMed:33068046,
CC ECO:0000269|PubMed:33224125}.
CC -!- ACTIVITY REGULATION: D-galactonate binds DgoR and induces a
CC conformational change in the protein, which decreases its affinity for
CC DNA and consequently derepresses transcription of the dgoRKADT operon.
CC {ECO:0000269|PubMed:30455279, ECO:0000269|PubMed:33068046,
CC ECO:0000269|PubMed:33224125}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:33068046}.
CC -!- INDUCTION: Part of the dgoRKADT operon, which encodes proteins for the
CC metabolism of D-galactonate (PubMed:211976, PubMed:30455279).
CC Negatively autoregulated (PubMed:30455279). {ECO:0000269|PubMed:211976,
CC ECO:0000269|PubMed:30455279}.
CC -!- DOMAIN: Contains an N-terminal DNA binding region and a C-terminal
CC effector-binding cavity (PubMed:33224125, PubMed:33068046). The C-
CC terminal region also contains a metal binding site (PubMed:33224125).
CC The divalent metal ion is not directly involved in the interaction with
CC DNA, but it plays an important role in interaction with D-galactonate
CC (PubMed:33224125). {ECO:0000269|PubMed:33068046,
CC ECO:0000269|PubMed:33224125}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene leads to faster growth of
CC E.coli in D-galactonate and results in a considerable increase in the
CC expression of dgo genes. {ECO:0000269|PubMed:30455279}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA62046.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L10328; AAA62046.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAT48199.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77599.1; -; Genomic_DNA.
DR RefSeq; WP_000174305.1; NZ_STEB01000015.1.
DR RefSeq; YP_026239.1; NC_000913.3.
DR PDB; 7C7E; X-ray; 2.05 A; A=1-229.
DR PDBsum; 7C7E; -.
DR AlphaFoldDB; P31460; -.
DR SMR; P31460; -.
DR BioGRID; 4263373; 13.
DR BioGRID; 853514; 1.
DR DIP; DIP-9435N; -.
DR STRING; 511145.b4479; -.
DR jPOST; P31460; -.
DR PaxDb; P31460; -.
DR PRIDE; P31460; -.
DR EnsemblBacteria; AAT48199; AAT48199; b4479.
DR EnsemblBacteria; BAE77599; BAE77599; BAE77599.
DR GeneID; 2847767; -.
DR GeneID; 66672407; -.
DR KEGG; ecj:JW5627; -.
DR KEGG; eco:b4479; -.
DR PATRIC; fig|1411691.4.peg.3008; -.
DR EchoBASE; EB1669; -.
DR eggNOG; COG2186; Bacteria.
DR HOGENOM; CLU_017584_9_4_6; -.
DR InParanoid; P31460; -.
DR OMA; DDPVPSH; -.
DR PhylomeDB; P31460; -.
DR BioCyc; EcoCyc:G7790-MON; -.
DR PRO; PR:P31460; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0000987; F:cis-regulatory region sequence-specific DNA binding; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc.
DR GO; GO:0001217; F:DNA-binding transcription repressor activity; IMP:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0098531; F:ligand-activated transcription factor activity; IDA:EcoCyc.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:EcoCyc.
DR GO; GO:0010677; P:negative regulation of cellular carbohydrate metabolic process; IMP:EcoCyc.
DR GO; GO:2000143; P:negative regulation of DNA-templated transcription, initiation; IMP:EcoCyc.
DR CDD; cd07377; WHTH_GntR; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 1.20.120.530; -; 1.
DR InterPro; IPR011711; GntR_C.
DR InterPro; IPR008920; TF_FadR/GntR_C.
DR InterPro; IPR000524; Tscrpt_reg_HTH_GntR.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF07729; FCD; 1.
DR Pfam; PF00392; GntR; 1.
DR PRINTS; PR00035; HTHGNTR.
DR SMART; SM00895; FCD; 1.
DR SMART; SM00345; HTH_GNTR; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR SUPFAM; SSF48008; SSF48008; 1.
DR PROSITE; PS50949; HTH_GNTR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Metal-binding; Reference proteome; Repressor;
KW Transcription; Transcription regulation; Zinc.
FT CHAIN 1..229
FT /note="Galactonate operon transcriptional repressor"
FT /id="PRO_0000050621"
FT DOMAIN 1..71
FT /note="HTH gntR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00307"
FT DNA_BIND 31..50
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00307"
FT BINDING 146
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:33224125,
FT ECO:0007744|PDB:7C7E"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:33224125,
FT ECO:0007744|PDB:7C7E"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:33224125,
FT ECO:0007744|PDB:7C7E"
FT MUTAGEN 7
FT /note="D->A: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 34
FT /note="L->A: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 40
FT /note="T->I: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 42
FT /note="R->C: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 46
FT /note="R->A: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 51
FT /note="S->L: Loss of DNA-binding ability and repressor
FT activity."
FT /evidence="ECO:0000269|PubMed:30455279"
FT MUTAGEN 102
FT /note="R->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 102
FT /note="R->Q: Completely non-responsive to D-galactonate.
FT Does not affect binding affinity for the dgo operator."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 106
FT /note="E->K: Completely non-responsive to D-galactonate.
FT Does not affect binding affinity for the dgo operator."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 146
FT /note="D->A: Shows increased DNA binding but can be
FT slightly reverted in the presence of D-galactonate. Strong
FT decrease in binding to D-galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 146
FT /note="D->N: Completely non-responsive to D-galactonate.
FT Shows a slight loss of repression ability."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 150
FT /note="H->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 150
FT /note="H->Y: Completely non-responsive to D-galactonate."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 173
FT /note="Q->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 179
FT /note="R->A: Shows no significant effect on the binding to
FT DNA and D-galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 181
FT /note="W->A: Shows no significant effect on the binding to
FT DNA and D-galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 184
FT /note="D->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 191
FT /note="T->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 191
FT /note="T->M: Completely non-responsive to D-galactonate.
FT Does not affect binding affinity for the dgo operator."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 192
FT /note="L->F: Completely non-responsive to D-galactonate.
FT Does not affect binding affinity for the dgo operator."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 195
FT /note="H->A: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 195
FT /note="H->Y: Completely non-responsive to D-galactonate."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 221
FT /note="S->A: Shows increased DNA binding but can be
FT slightly reverted in the presence of D-galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT MUTAGEN 221
FT /note="S->L: Decreases sensitivity to D-galactonate. Does
FT not affect binding affinity for the dgo operator."
FT /evidence="ECO:0000269|PubMed:33068046"
FT MUTAGEN 224
FT /note="R->A,E: Shows a decreased binding to both DNA and D-
FT galactonate."
FT /evidence="ECO:0000269|PubMed:33224125"
FT CONFLICT 111..112
FT /note="RW -> VA (in Ref. 1; AAA62046)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 229 AA; 26080 MW; EE41742299285B8F CRC64;
MTLNKTDRIV ITLGKQIVHG KYVPGSPLPA EAELCEEFAT SRNIIREVFR SLMAKRLIEM
KRYRGAFVAP RNQWNYLDTD VLQWVLENDY DPRLISAMSE VRNLVEPAIA RWAAERATSS
DLAQIESALN EMIANNQDRE AFNEADIRYH EAVLQSVHNP VLQQLSIAIS SLQRAVFERT
WMGDEANMPQ TLQEHKALFD AIRHQDGDAA EQAALTMIAS STRRLKEIT
