Summary: PRD domain
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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 ) and inactive state (1tlv ), revealing massive structural rearrangements upon activation.
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
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
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||regulation of transcription, DNA-dependent (GO:0006355)|
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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
We make a range of alignments for each Pfam-A family:
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|Seed source:||Pfam-B_772 (release 3.0)|
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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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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