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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 (493) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 743 3,271 11
Proteins 739 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) heterocycle metabolic process 0.0000000000009271 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000001142 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000004181 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000007552 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000000004771 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000003969 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000006401 Least Informative Direct
Biological Process (BP) biological regulation 0.02115 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00007341 Moderately Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) circadian rhythm 0.0000000001033 Highly Informative Direct
Molecular Function (MF) binding 0.3172 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00002477 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000006234 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000002743 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0000002945 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.0008447 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.09331 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000007277 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.01214 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2398 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.001141 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.08605 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.001373 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)
Biological processBiological rhythms0.000000000000005908InformativeDirect
Cellular componentNucleus0.0000000002415Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.000009488Least InformativeDirect
Post-translational modificationIsopeptide bond0.000001939Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000315Moderately 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 ]