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RBP11-like subunits of RNA polymerase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DCoH-like [ 55247] (5)
Superfamily:   RBP11-like subunits of RNA polymerase [ 55257] (2)
Families:   RBP11/RpoL [ 64311] (2)
  RNA polymerase alpha subunit dimerisation domain [ 55258] (2)


Superfamily statistics
Genomes (3,248) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 5,415 37,250 8
Proteins 5,400 37,144 8


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

Document:
Function annotation of SCOP domain superfamilies

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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.003388Least InformativeInherited
Worm Phenotype (WP)cell development variant0.004925Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0001463Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0004022Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0005021Moderately InformativeDirect
Worm Phenotype (WP)cell stress response variant0InformativeDirect
Worm Phenotype (WP)egg laying variant0InformativeDirect
Worm Phenotype (WP)hatching variant0Highly InformativeDirect
Worm Phenotype (WP)apoptosis reduced0Highly InformativeDirect
Worm Phenotype (WP)cell gamma ray response variant0Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)germ line cell0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009025 SSF55257 Protein matches
Abstract

RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and the prokaryotic RNAP alpha subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/betaż) can interact [PubMed11453250]. These different subunits share regions of homology. Rpb11 contains a domain (Rpb11-like domain) that is required for dimerisation, and binds to a homologous region on Rpb3. The Rpb11-like domain in Rpb11 and archaeal L subunits is contiguous, whereas in Rpb3, archaeal D, and prokaryotic alpha subunits , the Rpb11-like domain is interrupted by an insert domain . In the prokaryotic RNAP alpha subunit, the Rpb11-like domain and the insert domain form two subregions of the N-terminal domain.

The structure of the Rpb11-like domain consists of a two-layer alpha/beta fold consisting of beta(2)-alpha-beta(2)-alpha. Rpb3 and Rpb11 in yeast RNAP [PubMed11313498, PubMed12191485] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [PubMed9657722, PubMed12000971].


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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 7 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 RBP11-like subunits of RNA polymerase 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 7 hidden Markov models representing the RBP11-like subunits of RNA polymerase 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]