SUPERFAMILY 1.75 HMM library and genome assignments server


Eukaryotic DNA topoisomerase I, dispensable insert domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Long alpha-hairpin [ 46556] (20)
Superfamily:   Eukaryotic DNA topoisomerase I, dispensable insert domain [ 46596]
Families:   Eukaryotic DNA topoisomerase I, dispensable insert domain [ 46597]


Superfamily statistics
Genomes (139) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 248 848 10
Proteins 248 848 10


Functional annotation
General category Information
Detailed category DNA replication/repair

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 3.423e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.497e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.95e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.936e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 6.426e-06 Least Informative Direct
Biological Process (BP) DNA metabolic process 4.942e-11 Informative Direct
Molecular Function (MF) binding 0.09254 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0001051 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 1.267e-05 Informative Direct
Molecular Function (MF) chromatin binding 8.872e-09 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1.763e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.05356 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.008816 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 6.541e-08 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.005677 Moderately Informative Inherited
Cellular Component (CC) nucleolus 1.428e-05 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentNucleus4.705e-06Least InformativeDirect
Molecular functionDNA-binding2.846e-13Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein3.384e-05Least InformativeDirect
Post-translational modificationAcetylation5.354e-05Least InformativeDirect
Post-translational modificationIsopeptide bond1.932e-09Moderately InformativeDirect
Post-translational modificationUbl conjugation1.256e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009054 SSF46596 Protein matches
Abstract

Topoisomerase strand cleavage involves nucleophilic attack by a catalytic tyrosine residue, resulting in the enzyme being covalently attached to one end of the broken DNA strand. Eukaryotic DNA topoisomerase I is a multi-domain protein. The dispensable insert domain is the linker region that connects the central core of the enzyme to the C-terminal domain; it assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme [PubMed9488652].

More information about this protein can be found at Protein of the Month: DNA Topoisomerase.


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 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 DNA topoisomerase I, dispensable insert 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 DNA topoisomerase I, dispensable insert 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]