Summary: Bacterial regulatory proteins, luxR family
This is the Wikipedia entry entitled "LuxR-type DNA-binding HTH domain". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
LuxR-type DNA-binding HTH domain Edit Wikipedia article
|Bacterial regulatory proteins, luxR family|
|solution structure of the dna-binding domain of the erwinia amylovora rcsb protein|
In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. It is present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region of the protein; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.
The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers.
LuxR-type HTH proteins can be activated by one of four different mechanisms:
1. Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase. Some proteins that belong to this category are:
- Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis)
- Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis)
- Vibrio fischeri luxR (activates bioluminescence operon)
- E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes)
- Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene)
- Ducros VM, Lewis RJ, Verma CS, Dodson EJ, Leonard G, Turkenburg JP, Murshudov GN, Wilkinson AJ, Brannigan JA (March 2001). "Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis". J. Mol. Biol. 306 (4): 759–71. doi:10.1006/jmbi.2001.4443. PMID 11243786.
- Pristovsek P, Sengupta K, Lohr F, Schafer B, von Trebra MW, Ruterjans H, Bernhard F (May 2003). "Structural analysis of the DNA-binding domain of the Erwinia amylovora RcsB protein and its interaction with the RcsAB box". J. Biol. Chem. 278 (20): 17752–9. doi:10.1074/jbc.M301328200. PMID 12740396.
- Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A (June 2002). "Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA". Nature 417 (6892): 971–4. doi:10.1038/nature00833. PMID 12087407.
- Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE (October 2002). "Dimerization allows DNA target site recognition by the NarL response regulator". Nat. Struct. Biol. 9 (10): 771–8. doi:10.1038/nsb845. PMID 12352954.
- Birck C, Malfois M, Svergun D, Samama J (August 2002). "Insights into signal transduction revealed by the low resolution structure of the FixJ response regulator". J. Mol. Biol. 321 (3): 447–57. doi:10.1016/S0022-2836(02)00651-4. PMID 12162958.
- Pappas KM, Weingart CL, Winans SC (August 2004). "Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling". Mol. Microbiol. 53 (3): 755–69. doi:10.1111/j.1365-2958.2004.04212.x. PMID 15255890.
- Schlegel A, Bohm A, Lee SJ, Peist R, Decker K, Boos W (May 2002). "Network regulation of the Escherichia coli maltose system". J. Mol. Microbiol. Biotechnol. 4 (3): 301–7. PMID 11931562.
Bacterial regulatory proteins, luxR family Provide feedback
No Pfam abstract.
Internal database links
|Similarity to PfamA using HHSearch:||Sigma70_r4 Trans_reg_C HTH_10 HTH_5 HTH_7 LexA_DNA_bind Terminase_5 Sigma70_ECF HTH_11 Sigma70_r4_2 DUF2089 MarR_2 HTH_20 HTH_23 HTH_24 HTH_28 HTH_Tnp_ISL3 HTH_29 HTH_36 HTH_38 HTH_40|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000792
This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.
The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [PUBMED:11243786, PUBMED:12740396, PUBMED:12087407].
LuxR-type HTH proteins can be activated by one of four different mechanisms:
1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [PUBMED:12352954, PUBMED:12162958]. Some proteins that belong to this category are:
2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria [PUBMED:15255890]:
3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE [PUBMED:11243786].
4) Multiple ligand-binding regulators, exemplified by malT [PUBMED:11931562].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||intracellular (GO:0005622)|
|Molecular function||sequence-specific DNA binding (GO:0043565)|
|sequence-specific DNA binding transcription factor activity (GO:0003700)|
|Biological process||regulation of transcription, DNA-dependent (GO:0006355)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||30|
|Number in full:||38873|
|Average length of the domain:||57.10 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||20.74 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GerE domain has been found. There are 74 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...