SUPERFAMILY 1.75 HMM library and genome assignments server


RPB5-like RNA polymerase subunit superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   RPB5-like RNA polymerase subunit [ 55286]
Superfamily:   RPB5-like RNA polymerase subunit [ 55287]
Families:   RPB5 [ 55288] (2)


Superfamily statistics
Genomes (582) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 834 866 3
Proteins 833 865 3


Functional annotation
General category Information
Detailed category Transcription

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 7.391e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 8.825e-08 Least Informative Direct
Biological Process (BP) biosynthetic process 6.438e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000731 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0007412 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.007395 Least Informative Inherited
Biological Process (BP) gene expression 7.838e-13 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 2.052e-12 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.229e-12 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 2.297e-12 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.063e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.169e-11 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 2.183e-11 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 1.591e-06 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 9.746e-06 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 8.348e-11 Informative Direct
Molecular Function (MF) DNA-directed RNA polymerase activity 4.53e-15 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0003408 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) nucleoplasm part 9.566e-05 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 8.261e-14 Highly 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)DNA-directed RNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP 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)DNA-directed RNA polymerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentNucleus2.5e-05Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationTransferase1.001e-14Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000783 SSF55287 Protein matches
Abstract

Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region , plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [PubMed10841538, PubMed10191143, PubMed1729711, PubMed10841537].

This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2).


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) · Arabidopsis Plant Ontology (AP) · 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 3 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 RPB5-like RNA polymerase subunit 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 3 hidden Markov models representing the RPB5-like RNA polymerase subunit 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]