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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 (488) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 732 1,106 11
Proteins 728 1,095 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 0.000000000007986 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000004705 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000001468 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001482 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000000000672 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000000002147 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000002588 Least Informative Direct
Biological Process (BP) biological regulation 0.03271 Least Informative Inherited
Biological Process (BP) organelle organization 0.00004354 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00002671 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.04925 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) circadian rhythm 0.0000000000702 Highly Informative Direct
Biological Process (BP) chromosome organization 0 Highly Informative Direct
Molecular Function (MF) binding 0.4609 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.000009645 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000002181 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.00001594 Informative Direct
Molecular Function (MF) chromatin binding 0.0000001732 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000006931 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.06084 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000001332 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.009377 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1567 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0003932 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.04938 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00009755 Informative Direct
Cellular Component (CC) nucleolus 0.000000004466 Highly 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)
Biological processBiological rhythms0.000000000000005656InformativeDirect
Cellular componentNucleus0.0000000002199Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.000009549Least InformativeDirect
Post-translational modificationIsopeptide bond0.000001941Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00002785Moderately 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 ]