SUPERFAMILY 1.75 HMM library and genome assignments server

PTS-regulatory domain, PRD superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PTS-regulatory domain, PRD [ 63519]
Superfamily:   PTS-regulatory domain, PRD [ 63520]
Families:   PTS-regulatory domain, PRD [ 63521]

Superfamily statistics
Genomes (862) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 6,855 25,964 4
Proteins 4,213 16,793 2

Functional annotation
General category Information
Detailed category Transcription

Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Protein-N(pi)-phosphohistidine--sugar phosphotransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionRNA-binding2.894e-05Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationPhosphoprotein2.668e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011608 SSF63520 Protein matches

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, ) 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 [PubMed11751049, PubMed11733988, PubMed11447120].

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a PTS-regulatory domain, PRD domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the PTS-regulatory domain, PRD superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]