SUPERFAMILY 1.75 HMM library and genome assignments server


Rof/RNase P subunit-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Rof/RNase P subunit-like [ 101743]
Superfamily:   Rof/RNase P subunit-like [ 101744] (2)
Families:   RNase P subunit p29-like [ 101745] (3)
  Rof-like [ 141305]


Superfamily statistics
Genomes (887) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 955 2,240 5
Proteins 955 2,240 5


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 5.801e-05 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 6.535e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0001063 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0002026 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0005698 Least Informative Direct
Biological Process (BP) RNA metabolic process 2.316e-07 Moderately Informative Direct
Biological Process (BP) gene expression 4.187e-07 Moderately Informative Direct
Biological Process (BP) ncRNA metabolic process 5.744e-11 Informative Direct
Biological Process (BP) RNA processing 1.961e-09 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 1.344e-05 Informative Direct
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 9.391e-14 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0001247 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 2.712e-07 Moderately Informative Direct
Molecular Function (MF) nuclease activity 3.874e-11 Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 1.555e-15 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 1.18e-14 Highly Informative Direct
Cellular Component (CC) ribonucleoprotein complex 1.566e-07 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processtRNA processing0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002730 SSF101744 Protein matches
Abstract

This entry contains one of the subunits, Rpp29, of RNase P. The structure of the RNase P subunit, Rpp29, from Methanothermobacter thermoautotrophicus has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex [PubMed14673079].

RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme [PubMed14673079].


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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 4 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 Rof/RNase P subunit-like 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 4 hidden Markov models representing the Rof/RNase P subunit-like 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]