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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)DescriptionActionsGraphical viewLength
Binding sitei99Cis,cis-muconate or benzoate 11
Binding sitei128Cis,cis-muconate or benzoate 11
Binding sitei144Benzoate 21
Binding sitei160Benzoate 21
Binding sitei202Benzoate 21
Binding sitei293Benzoate 21

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi18 – 37H-T-H motifPROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Aromatic hydrocarbons catabolism, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

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
Proteomesi
  • UP000000430 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001055941 – 304HTH-type transcriptional regulator BenMAdd BLAST304

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

1304
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 15Combined sources13
Helixi18 – 24Combined sources7
Helixi29 – 43Combined sources15
Beta strandi51 – 54Combined sources4
Helixi59 – 86Combined sources28
Beta strandi91 – 96Combined sources6
Helixi98 – 102Combined sources5
Helixi105 – 114Combined sources10
Beta strandi120 – 125Combined sources6
Helixi128 – 136Combined sources9
Beta strandi141 – 147Combined sources7
Beta strandi154 – 169Combined sources16
Helixi173 – 177Combined sources5
Turni178 – 180Combined sources3
Helixi184 – 186Combined sources3
Turni187 – 189Combined sources3
Beta strandi190 – 194Combined sources5
Beta strandi198 – 202Combined sources5
Helixi203 – 212Combined sources10
Turni213 – 215Combined sources3
Beta strandi219 – 223Combined sources5
Helixi227 – 235Combined sources9
Beta strandi240 – 244Combined sources5
Helixi245 – 249Combined sources5
Beta strandi255 – 260Combined sources6
Beta strandi266 – 274Combined sources9
Helixi280 – 296Combined sources17
Turni302 – 304Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO68014.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 58HTH lysR-typePROSITE-ProRule annotationAdd BLAST58

Domaini

Contains a secondary binding site for benzoate in addition to a primary effector binding site that can accommodate 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

eggNOGiENOG4108KB2. Bacteria.
ENOG410XSY7. LUCA.
HOGENOMiHOG000233514.
OMAiEILHIAQ.
OrthoDBiPOG091H09F3.

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.
SUPFAMiSSF46785. SSF46785. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti157T → S in AAC46441 (PubMed:9573203).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF009224 Genomic DNA. Translation: AAC46441.1.
CR543861 Genomic DNA. Translation: CAG68299.1.
RefSeqiWP_004925500.1. NC_005966.1.

Genome annotation databases

EnsemblBacteriaiCAG68299; CAG68299; ACIAD1435.
GeneIDi25684005.
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.
RefSeqiWP_004925500.1. NC_005966.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi62977.ACIAD1435.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAG68299; CAG68299; ACIAD1435.
GeneIDi25684005.
KEGGiaci:ACIAD1435.
PATRICi20740682. VBIAciSp98416_1293.

Phylogenomic databases

eggNOGiENOG4108KB2. Bacteria.
ENOG410XSY7. LUCA.
HOGENOMiHOG000233514.
OMAiEILHIAQ.
OrthoDBiPOG091H09F3.

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.
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS50931. HTH_LYSR. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 2, 2016
This is version 107 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

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 one 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.