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11  structures 2053  species 1  interaction 15913  sequences 106  architectures

Family: PRD (PF00874)

Summary: PRD domain

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PRD domain Provide feedback

The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators PF03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (1h99 [2]) and inactive state (1tlv [4]), revealing massive structural rearrangements upon activation.

Literature references

  1. van Tilbeurgh H, Declerck N; , Curr Opin Struct Biol 2001;11:685-693.: Structural insights into the regulation of bacterial signalling proteins containing PRDs. PUBMED:11751049 EPMC:11751049

  2. van Tilbeurgh H, Le Coq D, Declerck N; , EMBO J 2001;20:3789-3799.: Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. PUBMED:11447120 EPMC:11447120

  3. Declerck N, Dutartre H, Receveur V, Dubois V, Royer C, Aymerich S, van Tilbeurgh H; , J Mol Biol 2001;314:671-681.: Dimer stabilization upon activation of the transcriptional antiterminator LicT. PUBMED:11733988 EPMC:11733988

  4. Graille M, Zhou CZ, Receveur-Brechot V, Collinet B, Declerck N, van Tilbeurgh H; , J Biol Chem. 2005;280:14780-14789.: Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. PUBMED:15699035 EPMC:15699035


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011608

Transcriptional antiterminators and activators containing phosphoenolpyruvate: sugar phosphotransferase system (PTS) regulation domains (PRDs) form a class of bacterial regulatory proteins whose activity is modulated by phosphorylation. These regulators stimulate the expression of genes and operons involved in carbohydrate metabolism.

PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria [PUBMED:1732212, PUBMED:9045813] and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators, INTERPRO) or DNA (for activators), and a duplicated PRD module which is phosphorylated on conserved histidines by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations are thought to modify the stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain [PUBMED:11751049, PUBMED:11733988, PUBMED:11447120].

PRDs are characterised by the presence of a duplicated regulatory module of ~100 residues that can be reversibly phosphorylated on histidyl residues by the PTS. PRDs in transcriptional antiterminators and activators are PTS regulatory targets that are (de)phosphorylated in response to the availability of carbon sources [PUBMED:9202047, PUBMED:9663674, PUBMED:11751049, PUBMED:11447120, PUBMED:15699035].

The PRD domain comprises one and often two highly conserved histidines. It forms a compact bundle comprising five helices (alpha1-alpha5). The core of the PRD module consists of two pairs of antiparallel helices making an angle of ~60 degrees. The first pair contains the antiparallel helices alpha1 and alpha4, while the second pair contains alpha2 and alpha5. The third helix (alpha3) is oriented perpendicularly to alpha5 at the periphery of the bundle. The helices are connected by loops of varying length [PUBMED:11751049, PUBMED:11447120, PUBMED:15699035].

Gene Ontology

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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 PRD (CL0166), which has the following description:

The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator of the BglG family as well as in activators such as MtlR and LevR. The PRD domain is phosphorylated on a conserved histidine residue. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators (Pfam:PF03123, see also comments for this family)) or DNA (for activators), and a duplicated PRD module which is phosphorylated on conserved histidines by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations are thought to modify the stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain.

The clan contains the following 2 members:

PRD PRD_Mga

Alignments

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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
(211)
Full
(15913)
Representative proteomes NCBI
(9078)
Meta
(56)
RP15
(437)
RP35
(816)
RP55
(1106)
RP75
(1448)
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Format an alignment

  Seed
(211)
Full
(15913)
Representative proteomes NCBI
(9078)
Meta
(56)
RP15
(437)
RP35
(816)
RP55
(1106)
RP75
(1448)
Alignment:
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Sequence:
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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
(211)
Full
(15913)
Representative proteomes NCBI
(9078)
Meta
(56)
RP15
(437)
RP35
(816)
RP55
(1106)
RP75
(1448)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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 View help on the curation process

Seed source: Pfam-B_772 (release 3.0)
Previous IDs: BglG_antitermin;
Type: Domain
Author: Declerck N, Bateman A
Number in seed: 211
Number in full: 15913
Average length of the domain: 90.60 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 28.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 89
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

PRD

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 PRD domain has been found. There are 11 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.

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