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Ribonuclease PH domain 2-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ribonuclease PH domain 2-like [ 55665]
Superfamily:   Ribonuclease PH domain 2-like [ 55666]
Families:   Ribonuclease PH domain 2-like [ 55667] (10)


Superfamily statistics
Genomes (3,045) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 10,165 50,328 21
Proteins 7,447 34,504 20


Functional annotation
General category Metabolism
Detailed category Nucleotide 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 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000003734 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000000001763 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000001243 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0001146 Least Informative Direct
Biological Process (BP) biological regulation 0.1277 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02822 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000000000000007296 Moderately Informative Direct
Biological Process (BP) gene expression 0.000003447 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0000952 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8216 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6977 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8706 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.001637 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1717 Moderately Informative Inherited
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) ncRNA processing 0.0001267 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0006005 Informative Direct
Biological Process (BP) immune effector process 0.0008181 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.06321 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.1779 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.004574 Informative Inherited
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of RNA stability 0.00000000000001422 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.00003034 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0.0001063 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 1 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00002611 Least Informative Direct
Molecular Function (MF) transferase activity 0.02544 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0000000131 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.01046 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.000001217 Informative Direct
Cellular Component (CC) intracellular organelle part 0.08002 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1429 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00004041 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.00006015 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processtRNA processing0InformativeDirect
Biological processrRNA processing0.0001109InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentExosome0Highly InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0.006022Moderately InformativeInherited
Post-translational modificationExonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015847 SSF55666 Protein matches
Abstract

This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes. [PubMed9390555].

More information about these proteins can be found at Protein of the Month: RNA Exosomes.


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) · 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 15 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 Ribonuclease PH domain 2-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 15 hidden Markov models representing the Ribonuclease PH domain 2-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) · UniProtKB KeyWords (KW) · Internal database links ]