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 (486) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 729 1,106 11
Proteins 725 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 0.00000000006727 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000001169 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000001309 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000000005042 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000000002248 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.003644 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01647 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002684 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0.0001813 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0002745 Moderately Informative Direct
Biological Process (BP) chromosome organization 0.0000000005688 Informative Direct
Biological Process (BP) circadian rhythm 0.0000000002162 Highly Informative Direct
Molecular Function (MF) binding 0.5877 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00002192 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000006105 Informative Direct
Molecular Function (MF) chromatin binding 0.0000005955 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000006425 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.02584 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000008351 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.228 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.04902 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000001669 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.04883 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.002735 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 componentNucleus0.000000001002Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.0000007063Least InformativeDirect
Post-translational modificationIsopeptide bond0.000000002032Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000002476Moderately 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 ]