BENM_ACIAD
ID BENM_ACIAD Reviewed; 304 AA.
AC O68014; Q6FCB2;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 31-AUG-2004, sequence version 2.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=HTH-type transcriptional regulator BenM;
DE AltName: Full=Ben and cat operon transcriptional regulator;
GN Name=benM; Synonyms=benR; OrderedLocusNames=ACIAD1435;
OS Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellales; Moraxellaceae;
OC Acinetobacter.
OX NCBI_TaxID=62977;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9573203; DOI=10.1128/jb.180.9.2493-2501.1998;
RA Collier L.S., Gaines G.L. III, Neidel E.L.;
RT "Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by
RT BenM, a LysR-type transcriptional activator.";
RL J. Bacteriol. 180:2493-2501(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33305 / BD413 / ADP1;
RX PubMed=15514110; DOI=10.1093/nar/gkh910;
RA Barbe V., Vallenet D., Fonknechten N., Kreimeyer A., Oztas S., Labarre L.,
RA Cruveiller S., Robert C., Duprat S., Wincker P., Ornston L.N.,
RA Weissenbach J., Marliere P., Cohen G.N., Medigue C.;
RT "Unique features revealed by the genome sequence of Acinetobacter sp. ADP1,
RT a versatile and naturally transformation competent bacterium.";
RL Nucleic Acids Res. 32:5766-5779(2004).
RN [3] {ECO:0007744|PDB:2F8D, ECO:0007744|PDB:2F97}
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 81-304 IN COMPLEX WITH THE
RP EFFECTOR BENZOATE, AND SUBUNIT.
RX PubMed=17565172; DOI=10.1107/s1744309107019185;
RA Ezezika O.C., Haddad S., Neidle E.L., Momany C.;
RT "Oligomerization of BenM, a LysR-type transcriptional regulator: structural
RT basis for the aggregation of proteins in this family.";
RL Acta Crystallogr. F 63:361-368(2007).
RN [4] {ECO:0007744|PDB:2F6G, ECO:0007744|PDB:2F6P, ECO:0007744|PDB:2F78, ECO:0007744|PDB:2F7A}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 81-304 IN COMPLEXES WITH THE
RP EFFECTORS BENZOATE AND CIS,CIS-MUCONATE, AND DOMAIN.
RX PubMed=17291527; DOI=10.1016/j.jmb.2006.09.090;
RA Ezezika O.C., Haddad S., Clark T.J., Neidle E.L., Momany C.;
RT "Distinct effector-binding sites enable synergistic transcriptional
RT activation by BenM, a LysR-type regulator.";
RL J. Mol. Biol. 367:616-629(2007).
CC -!- FUNCTION: Positive regulator of the ben and cat genes for benzoate
CC degradation. BenM is necessary for ben gene expression but not for
CC expression of the cat genes, which can be regulated by CatM. Binds to
CC the inducers cis,cis-muconate and benzoate.
CC -!- SUBUNIT: Homotetramer; dimer of dimers. The dimers can also associate
CC to form linear, higher oligomers (in vitro).
CC {ECO:0000269|PubMed:17565172}.
CC -!- DOMAIN: Contains a secondary binding site for benzoate in addition to a
CC primary effector binding site that can accommodate either cis,cis-
CC muconate or benzoate. The existence of this secondary binding site may
CC explain the synergistic effects of cis,cis-muconate and benzoate.
CC {ECO:0000269|PubMed:17291527}.
CC -!- SIMILARITY: Belongs to the LysR transcriptional regulatory family.
CC {ECO:0000305}.
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DR EMBL; AF009224; AAC46441.1; -; Genomic_DNA.
DR EMBL; CR543861; CAG68299.1; -; Genomic_DNA.
DR RefSeq; WP_004925500.1; NC_005966.1.
DR PDB; 2F6G; X-ray; 1.91 A; A/B=81-304.
DR PDB; 2F6P; X-ray; 2.00 A; A/B=81-304.
DR PDB; 2F78; X-ray; 2.05 A; A/B=81-304.
DR PDB; 2F7A; X-ray; 1.90 A; A/B=81-304.
DR PDB; 2F8D; X-ray; 2.70 A; A/B=81-304.
DR PDB; 2F97; X-ray; 2.20 A; A=81-304.
DR PDB; 2H99; X-ray; 1.85 A; A/B=1-304.
DR PDB; 2H9B; X-ray; 1.80 A; A/B=1-304.
DR PDB; 3K1M; X-ray; 2.29 A; A/B=1-304.
DR PDB; 3K1N; X-ray; 2.99 A; A/B=1-304.
DR PDB; 3K1P; X-ray; 3.00 A; A/B=1-304.
DR PDB; 3M1E; X-ray; 1.80 A; A=1-87.
DR PDB; 4IHS; X-ray; 3.10 A; A/B/C/D=1-87.
DR PDB; 4IHT; X-ray; 3.00 A; A/B/C/D=1-87.
DR PDBsum; 2F6G; -.
DR PDBsum; 2F6P; -.
DR PDBsum; 2F78; -.
DR PDBsum; 2F7A; -.
DR PDBsum; 2F8D; -.
DR PDBsum; 2F97; -.
DR PDBsum; 2H99; -.
DR PDBsum; 2H9B; -.
DR PDBsum; 3K1M; -.
DR PDBsum; 3K1N; -.
DR PDBsum; 3K1P; -.
DR PDBsum; 3M1E; -.
DR PDBsum; 4IHS; -.
DR PDBsum; 4IHT; -.
DR AlphaFoldDB; O68014; -.
DR SMR; O68014; -.
DR STRING; 62977.ACIAD1435; -.
DR EnsemblBacteria; CAG68299; CAG68299; ACIAD1435.
DR GeneID; 45233848; -.
DR KEGG; aci:ACIAD1435; -.
DR eggNOG; COG0583; Bacteria.
DR HOGENOM; CLU_039613_6_4_6; -.
DR OMA; DNTRRIG; -.
DR OrthoDB; 1439189at2; -.
DR BioCyc; ASP62977:ACIAD_RS06630-MON; -.
DR EvolutionaryTrace; O68014; -.
DR Proteomes; UP000000430; 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:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR005119; LysR_subst-bd.
DR InterPro; IPR000847; Tscrpt_reg_HTH_LysR.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF00126; HTH_1; 1.
DR Pfam; PF03466; LysR_substrate; 1.
DR PRINTS; PR00039; HTHLYSR.
DR SUPFAM; SSF46785; SSF46785; 1.
DR PROSITE; PS50931; HTH_LYSR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; Aromatic hydrocarbons catabolism; DNA-binding;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..304
FT /note="HTH-type transcriptional regulator BenM"
FT /id="PRO_0000105594"
FT DOMAIN 1..58
FT /note="HTH lysR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00253"
FT DNA_BIND 18..37
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00253"
FT BINDING 99
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:2F78, ECO:0007744|PDB:2F8D"
FT BINDING 99
FT /ligand="cis,cis-muconate"
FT /ligand_id="ChEBI:CHEBI:32379"
FT /evidence="ECO:0007744|PDB:2F7A"
FT BINDING 104
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:2F78, ECO:0007744|PDB:2F7A"
FT BINDING 128
FT /ligand="cis,cis-muconate"
FT /ligand_id="ChEBI:CHEBI:32379"
FT /evidence="ECO:0007744|PDB:2F7A"
FT BINDING 144
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:2F78"
FT BINDING 160
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:2F78, ECO:0007744|PDB:2F7A"
FT BINDING 202
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:2F7A"
FT BINDING 203
FT /ligand="cis,cis-muconate"
FT /ligand_id="ChEBI:CHEBI:32379"
FT /evidence="ECO:0007744|PDB:2F7A"
FT BINDING 293
FT /ligand="benzoate"
FT /ligand_id="ChEBI:CHEBI:16150"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:2F78, ECO:0007744|PDB:2F7A"
FT CONFLICT 157
FT /note="T -> S (in Ref. 1; AAC46441)"
FT /evidence="ECO:0000305"
FT HELIX 3..15
FT /evidence="ECO:0007829|PDB:3M1E"
FT HELIX 18..24
FT /evidence="ECO:0007829|PDB:3M1E"
FT HELIX 29..43
FT /evidence="ECO:0007829|PDB:3M1E"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:4IHS"
FT HELIX 59..86
FT /evidence="ECO:0007829|PDB:3M1E"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 98..102
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 154..169
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:2H9B"
FT TURN 178..180
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:2H9B"
FT TURN 187..189
FT /evidence="ECO:0007829|PDB:3K1P"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 198..202
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 203..212
FT /evidence="ECO:0007829|PDB:2H9B"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 227..235
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 240..244
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 245..249
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 255..260
FT /evidence="ECO:0007829|PDB:2H9B"
FT STRAND 266..274
FT /evidence="ECO:0007829|PDB:2H9B"
FT HELIX 280..296
FT /evidence="ECO:0007829|PDB:2H9B"
FT TURN 302..304
FT /evidence="ECO:0007829|PDB:2F7A"
SQ SEQUENCE 304 AA; 34532 MW; 23E5837E73039122 CRC64;
MELRHLRYFV AVVEEQSFTK AADKLCIAQP PLSRQIQNLE EELGIQLLER GSRPVKTTPE
GHFFYQYAIK LLSNVDQMVS MTKRIASVEK TIRIGFVGSL LFGLLPRIIH LYRQAHPNLR
IELYEMGTKA QTEALKEGRI DAGFGRLKIS DPAIKRTLLR NERLMVAVHA SHPLNQMKDK
GVHLNDLIDE KILLYPSSPK PNFSTHVMNI FSDHGLEPTK INEVREVQLA LGLVAAGEGI
SLVPASTQSI QLFNLSYVPL LDPDAITPIY IAVRNMEEST YIYSLYETIR QIYAYEGFTE
PPNW
