Summary: Lrp/AsnC ligand binding domain
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Lrp/AsnC ligand binding domain Provide feedback
The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold [2].
Literature references
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Kyrpides NC, Ouzounis CA; , Trends Biochem Sci 1995;20:140-141.: The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. PUBMED:7770911 EPMC:7770911
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Ren J, Sainsbury S, Combs SE, Capper RG, Jordan PW, Berrow NS, Stammers DK, Saunders NJ, Owens RJ;, J Biol Chem. 2007;282:14655-14664.: The structure and transcriptional analysis of a global regulator from Neisseria meningitidis. PUBMED:17374605 EPMC:17374605
Internal database links
SCOOP: | AsnC_trans_reg2 BAT GYD NapD PrgU |
Similarity to PfamA using HHSearch: | NapD GYD AsnC_trans_reg2 |
External database links
PROSITE: | PDOC00520 |
SCOP: | 1i1g |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019887
The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily [PUBMED:7770911]. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes [PUBMED:12675791].
Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [PUBMED:12675791].
This entry represents the C-terminal regulatory ligand binding domain of the transcription regulator AsnC/Lrp. Structurally this domain has a dimeric alpha/beta barrel fold [PUBMED:7770911, PUBMED:17374605].Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Dim_A_B_barrel (CL0032), which has the following description:
This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.
The clan contains the following 28 members:
ABM AsnC_trans_reg AsnC_trans_reg2 Chalcone_N Chlor_dismutase Cyclase_polyket Dabb Dehydratase_hem DUF1330 DUF1428 DUF3291 DUF4188 DUF4242 DUF4937 Dyp_perox EthD FtsX_ECD GYD HapK MIase MmlI NapD NIPSNAP rhaM SchA_CurD SOR YCII ydhRAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (237) |
Full (33553) |
Representative proteomes | UniProt (90767) |
NCBI (98303) |
Meta (2157) |
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RP15 (5215) |
RP35 (19360) |
RP55 (33667) |
RP75 (51876) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (237) |
Full (33553) |
Representative proteomes | UniProt (90767) |
NCBI (98303) |
Meta (2157) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (5215) |
RP35 (19360) |
RP55 (33667) |
RP75 (51876) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_773 (release 3.0) |
Previous IDs: | ASNC_trans_reg; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 237 |
Number in full: | 33553 |
Average length of the domain: | 73.00 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 47.37 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 75 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
Structures
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 AsnC_trans_reg domain has been found. There are 128 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 sequence.
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