Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

O68014

- BENM_ACIAD

UniProt

O68014 - BENM_ACIAD

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

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

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 – 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

        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:
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

« 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: October 29, 2014
This is version 94 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