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Protein

HTH-type transcriptional regulator BenM

Gene

benM

Organism
Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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
Complete GO annotation...

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 – 1513Combined sources
Helixi18 – 247Combined sources
Helixi29 – 4315Combined sources
Beta strandi51 – 544Combined sources
Helixi59 – 8628Combined sources
Beta strandi91 – 966Combined sources
Helixi98 – 1025Combined sources
Helixi105 – 11410Combined sources
Beta strandi120 – 1256Combined sources
Helixi128 – 1369Combined sources
Beta strandi141 – 1477Combined sources
Beta strandi154 – 16916Combined sources
Helixi173 – 1775Combined sources
Turni178 – 1803Combined sources
Helixi184 – 1863Combined sources
Turni187 – 1893Combined sources
Beta strandi190 – 1945Combined sources
Beta strandi198 – 2025Combined sources
Helixi203 – 21210Combined sources
Turni213 – 2153Combined sources
Beta strandi219 – 2235Combined sources
Helixi227 – 2359Combined sources
Beta strandi240 – 2445Combined sources
Helixi245 – 2495Combined sources
Beta strandi255 – 2606Combined sources
Beta strandi266 – 2749Combined sources
Helixi280 – 29617Combined sources
Turni302 – 3043Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
OMAiGRFFHEH.
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

        10         20         30         40         50
MELRHLRYFV AVVEEQSFTK AADKLCIAQP PLSRQIQNLE EELGIQLLER
60 70 80 90 100
GSRPVKTTPE GHFFYQYAIK LLSNVDQMVS MTKRIASVEK TIRIGFVGSL
110 120 130 140 150
LFGLLPRIIH LYRQAHPNLR IELYEMGTKA QTEALKEGRI DAGFGRLKIS
160 170 180 190 200
DPAIKRTLLR NERLMVAVHA SHPLNQMKDK GVHLNDLIDE KILLYPSSPK
210 220 230 240 250
PNFSTHVMNI FSDHGLEPTK INEVREVQLA LGLVAAGEGI SLVPASTQSI
260 270 280 290 300
QLFNLSYVPL LDPDAITPIY IAVRNMEEST YIYSLYETIR QIYAYEGFTE

PPNW
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
AF009224 Genomic DNA. Translation: AAC46441.1.
CR543861 Genomic DNA. Translation: CAG68299.1.
RefSeqiYP_046121.1. NC_005966.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

STRINGi62977.ACIAD1435.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0583.
HOGENOMiHOG000233514.
OMAiGRFFHEH.
OrthoDBiEOG686NGM.

Enzyme and pathway databases

BioCyciASP62977:GJVV-1363-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO68014.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: January 7, 2015
This is version 96 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.