SUPERFAMILY 1.75 HMM library and genome assignments server


Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [ 46915]
Families:   Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [ 46916]


Superfamily statistics
Genomes (1,848) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,918 12,637 2
Proteins 1,918 12,637 2


Functional annotation
General category Information
Detailed category RNA processing

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) cellular aromatic compound metabolic process 6.226e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001965 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0005505 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 5.553e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000102 Least Informative Direct
Biological Process (BP) response to stimulus 0.02375 Least Informative Inherited
Biological Process (BP) RNA metabolic process 2.135e-07 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0002189 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 0.00011 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0003221 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 6.278e-06 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 1.191e-05 Informative Direct
Molecular Function (MF) transferase activity 4.595e-06 Least Informative Direct
Molecular Function (MF) binding 0.01976 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.004618 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 9.519e-08 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 2.835e-07 Moderately Informative Direct
Molecular Function (MF) nuclease activity 4.026e-11 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 1.056e-13 Informative Direct
Cellular Component (CC) cytoplasmic part 2.684e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.007601 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002906 Least Informative Inherited
Cellular Component (CC) organelle envelope 2.709e-06 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 4.773e-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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately 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)
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015848 SSF46915 Protein matches
Abstract

This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 and PH domain 2 , both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle.

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) · 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 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 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 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 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 ]