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O68014

- BENM_ACIAD

UniProt

O68014 - BENM_ACIAD

Protein

HTH-type transcriptional regulator BenM

Gene

benM

Organism
Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 93 (01 Oct 2014)
      Sequence version 2 (31 Aug 2004)
      Previous versions | rss
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    Functioni

    Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei99 – 991Cis,cis-muconate or benzoate 1
    Binding sitei128 – 1281Cis,cis-muconate or benzoate 1
    Binding sitei144 – 1441Benzoate 2
    Binding sitei160 – 1601Benzoate 2
    Binding sitei202 – 2021Benzoate 2
    Binding sitei293 – 2931Benzoate 2

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi18 – 3720H-T-H motifPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. sequence-specific DNA binding transcription factor activity Source: InterPro

    GO - Biological processi

    1. aromatic compound catabolic process Source: UniProtKB-KW
    2. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciASP62977:GJVV-1363-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    HTH-type transcriptional regulator BenM
    Alternative name(s):
    Ben and cat operon transcriptional regulator
    Gene namesi
    Name:benM
    Synonyms:benR
    Ordered Locus Names:ACIAD1435
    OrganismiAcinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
    Taxonomic identifieri62977 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaeAcinetobacter
    ProteomesiUP000000430: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 304304HTH-type transcriptional regulator BenMPRO_0000105594Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers. The dimers can also associate to form linear, higher oligomers (in vitro).1 Publication

    Protein-protein interaction databases

    STRINGi62977.ACIAD1435.

    Structurei

    Secondary structure

    1
    304
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1513
    Helixi18 – 247
    Helixi29 – 4315
    Beta strandi51 – 544
    Helixi59 – 8628
    Beta strandi91 – 966
    Helixi98 – 1025
    Helixi105 – 11410
    Beta strandi120 – 1256
    Helixi128 – 1369
    Beta strandi141 – 1477
    Beta strandi154 – 16916
    Helixi173 – 1775
    Turni178 – 1803
    Helixi184 – 1863
    Turni187 – 1893
    Beta strandi190 – 1945
    Beta strandi198 – 2025
    Helixi203 – 21210
    Turni213 – 2153
    Beta strandi219 – 2235
    Helixi227 – 2359
    Beta strandi240 – 2445
    Helixi245 – 2495
    Beta strandi255 – 2606
    Beta strandi266 – 2749
    Helixi280 – 29617
    Turni302 – 3043

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2F6GX-ray1.91A/B81-304[»]
    2F6PX-ray2.00A/B81-304[»]
    2F78X-ray2.05A/B81-304[»]
    2F7AX-ray1.90A/B81-304[»]
    2F8DX-ray2.70A/B81-304[»]
    2F97X-ray2.20A81-304[»]
    2H99X-ray1.85A/B1-304[»]
    2H9BX-ray1.80A/B1-304[»]
    3K1MX-ray2.29A/B1-304[»]
    3K1NX-ray2.99A/B1-304[»]
    3K1PX-ray3.00A/B1-304[»]
    3M1EX-ray1.80A1-87[»]
    4IHSX-ray3.10A/B/C/D1-87[»]
    4IHTX-ray3.00A/B/C/D1-87[»]
    ProteinModelPortaliO68014.
    SMRiO68014. Positions 84-304.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO68014.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 5858HTH lysR-typePROSITE-ProRule annotationAdd
    BLAST

    Domaini

    Contains a secondary binding site for benzoate in addition to a primary effector binding site that can accomodate either cis,cis-muconate or benzoate. The existence of this secondary binding site may explain the synergistic effects of cis,cis-muconate and benzoate.1 Publication

    Sequence similaritiesi

    Contains 1 HTH lysR-type DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0583.
    HOGENOMiHOG000233514.
    OMAiDTGRFFY.
    OrthoDBiEOG686NGM.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    InterProiIPR005119. LysR_subst-bd.
    IPR000847. Tscrpt_reg_HTH_LysR.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF00126. HTH_1. 1 hit.
    PF03466. LysR_substrate. 1 hit.
    [Graphical view]
    PRINTSiPR00039. HTHLYSR.
    PROSITEiPS50931. HTH_LYSR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O68014-1 [UniParc]FASTAAdd to Basket

    « Hide

    MELRHLRYFV AVVEEQSFTK AADKLCIAQP PLSRQIQNLE EELGIQLLER    50
    GSRPVKTTPE GHFFYQYAIK LLSNVDQMVS MTKRIASVEK TIRIGFVGSL 100
    LFGLLPRIIH LYRQAHPNLR IELYEMGTKA QTEALKEGRI DAGFGRLKIS 150
    DPAIKRTLLR NERLMVAVHA SHPLNQMKDK GVHLNDLIDE KILLYPSSPK 200
    PNFSTHVMNI FSDHGLEPTK INEVREVQLA LGLVAAGEGI SLVPASTQSI 250
    QLFNLSYVPL LDPDAITPIY IAVRNMEEST YIYSLYETIR QIYAYEGFTE 300
    PPNW 304
    Length:304
    Mass (Da):34,532
    Last modified:August 31, 2004 - v2
    Checksum:i23E5837E73039122
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti157 – 1571T → S in AAC46441. (PubMed:9573203)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF009224 Genomic DNA. Translation: AAC46441.1.
    CR543861 Genomic DNA. Translation: CAG68299.1.
    RefSeqiYP_046121.1. NC_005966.1.

    Genome annotation databases

    EnsemblBacteriaiCAG68299; CAG68299; ACIAD1435.
    GeneIDi2880312.
    KEGGiaci:ACIAD1435.
    PATRICi20740682. VBIAciSp98416_1293.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF009224 Genomic DNA. Translation: AAC46441.1 .
    CR543861 Genomic DNA. Translation: CAG68299.1 .
    RefSeqi YP_046121.1. NC_005966.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2F6G X-ray 1.91 A/B 81-304 [» ]
    2F6P X-ray 2.00 A/B 81-304 [» ]
    2F78 X-ray 2.05 A/B 81-304 [» ]
    2F7A X-ray 1.90 A/B 81-304 [» ]
    2F8D X-ray 2.70 A/B 81-304 [» ]
    2F97 X-ray 2.20 A 81-304 [» ]
    2H99 X-ray 1.85 A/B 1-304 [» ]
    2H9B X-ray 1.80 A/B 1-304 [» ]
    3K1M X-ray 2.29 A/B 1-304 [» ]
    3K1N X-ray 2.99 A/B 1-304 [» ]
    3K1P X-ray 3.00 A/B 1-304 [» ]
    3M1E X-ray 1.80 A 1-87 [» ]
    4IHS X-ray 3.10 A/B/C/D 1-87 [» ]
    4IHT X-ray 3.00 A/B/C/D 1-87 [» ]
    ProteinModelPortali O68014.
    SMRi O68014. Positions 84-304.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 62977.ACIAD1435.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAG68299 ; CAG68299 ; ACIAD1435 .
    GeneIDi 2880312.
    KEGGi aci:ACIAD1435.
    PATRICi 20740682. VBIAciSp98416_1293.

    Phylogenomic databases

    eggNOGi COG0583.
    HOGENOMi HOG000233514.
    OMAi DTGRFFY.
    OrthoDBi EOG686NGM.

    Enzyme and pathway databases

    BioCyci ASP62977:GJVV-1363-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O68014.

    Family and domain databases

    Gene3Di 1.10.10.10. 1 hit.
    InterProi IPR005119. LysR_subst-bd.
    IPR000847. Tscrpt_reg_HTH_LysR.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view ]
    Pfami PF00126. HTH_1. 1 hit.
    PF03466. LysR_substrate. 1 hit.
    [Graphical view ]
    PRINTSi PR00039. HTHLYSR.
    PROSITEi PS50931. HTH_LYSR. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator."
      Collier L.S., Gaines G.L. III, Neidel E.L.
      J. Bacteriol. 180:2493-2501(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium."
      Barbe V., Vallenet D., Fonknechten N., Kreimeyer A., Oztas S., Labarre L., Cruveiller S., Robert C., Duprat S., Wincker P., Ornston L.N., Weissenbach J., Marliere P., Cohen G.N., Medigue C.
      Nucleic Acids Res. 32:5766-5779(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 33305 / BD413 / ADP1.
    3. "Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family."
      Ezezika O.C., Haddad S., Neidle E.L., Momany C.
      Acta Crystallogr. F 63:361-368(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 81-304 IN COMPLEX WITH THE EFFECTOR BENZOATE, SUBUNIT.
    4. "Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator."
      Ezezika O.C., Haddad S., Clark T.J., Neidle E.L., Momany C.
      J. Mol. Biol. 367:616-629(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 81-304 IN COMPLEXES WITH THE EFFECTORS BENZOATE AND CIS,CIS-MUCONATE, DOMAIN.

    Entry informationi

    Entry nameiBENM_ACIAD
    AccessioniPrimary (citable) accession number: O68014
    Secondary accession number(s): Q6FCB2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: August 31, 2004
    Last modified: October 1, 2014
    This is version 93 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3