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Eukaryotic RPB5 N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Restriction endonuclease-like [ 52979] (4)
Superfamily:   Eukaryotic RPB5 N-terminal domain [ 53036]
Families:   Eukaryotic RPB5 N-terminal domain [ 53037]


Superfamily statistics
Genomes (485) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 830 2,188 1
Proteins 820 2,167 1


Functional annotation
General category Information
Detailed category Transcription

Document:
Function annotation of SCOP domain superfamilies

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

InterPro annotation
Cross references IPR005571 SSF53036 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 the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [PubMed10784442]. This module is important for positioning the downstream DNA.


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 · Arabidopsis Plant Ontology (AP) ]

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 1 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 Eukaryotic RPB5 N-terminal domain 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 1 hidden Markov models representing the Eukaryotic RPB5 N-terminal domain 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 · Arabidopsis Plant Ontology (AP) · Internal database links ]