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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 (495) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 749 3,271 11
Proteins 745 3,256 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 0.000000000001973 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000001294 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000007138 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001049 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000000001613 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000000001346 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000000723 Least Informative Direct
Biological Process (BP) biological regulation 0.02988 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01357 Least Informative Inherited
Biological Process (BP) organelle organization 0.000000000000003734 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0001038 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) circadian rhythm 0.000000000132 Highly Informative Direct
Molecular Function (MF) binding 0.2585 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00003498 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000009815 Informative Direct
Molecular Function (MF) chromatin binding 0.0000005903 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000004359 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.001057 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.1031 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000002531 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.01253 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2374 Least Informative Inherited
Cellular Component (CC) nuclear part 0.08902 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.001151 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.001212 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processBiological rhythms0.000000000000005672InformativeDirect
Cellular componentNucleus0.0000000002502Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.000001004Least InformativeDirect
Post-translational modificationIsopeptide bond0.00002671Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0001943Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]