SUPERFAMILY 1.75 HMM library and genome assignments server


Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [ 56740]
Superfamily:   Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [ 56741]
Families:   Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [ 56742]


Superfamily statistics
Genomes (474) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 695 0 11
Proteins 691 0 11


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 7.436e-11 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.244e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.772e-08 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 5.56e-11 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.482e-10 Least Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Molecular Function (MF) binding 0.8369 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0006948 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 6.642e-05 Informative Direct
Molecular Function (MF) chromatin binding 5.115e-07 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1.503e-11 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.3961 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.09131 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 5.562e-07 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1571 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.003156 Informative Inherited

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 componentNucleus9.934e-10Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein6.886e-07Least InformativeDirect
Post-translational modificationIsopeptide bond1.695e-09Moderately InformativeDirect
Post-translational modificationUbl conjugation2.251e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008336 SSF56741 Protein matches
Abstract

This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain [PubMed14741206]. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes [PubMed9488644].

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 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 Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment 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 Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment 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 ]