Summary: Topoisomerase DNA binding C4 zinc finger
Topoisomerase DNA binding C4 zinc finger Provide feedback
No Pfam abstract.
Ahumada A, Tse-Dinh YC; , Biochem Biophys Res Commun 1998;251:509-514.: The Zn(II) binding motifs of E. coli DNA topoisomerase I is part of a high-affinity DNA binding domain. PUBMED:9792804 EPMC:9792804
Internal database links
|Similarity to PfamA using HHSearch:||Ogr_Delta RNA_POL_M_15KD DUF1936|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013498
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [PUBMED:7770916]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [PUBMED:12042765, PUBMED:11395412]. DNA topoisomerases are divided into two classes: type I enzymes (EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (EC; topoisomerases II, IV and VI) break double-strand DNA [PUBMED:12596227].
Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.
This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc [PUBMED:10873443]. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc.
More information about this protein can be found at Protein of the Month: DNA Topoisomerase [PUBMED:].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||chromosome (GO:0005694)|
|Molecular function||DNA binding (GO:0003677)|
|DNA topoisomerase activity (GO:0003916)|
|Biological process||DNA topological change (GO:0006265)|
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A clan of zinc-binding ribbon domains.
The clan contains the following 50 members:A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C DNA_RNApol_7kD DUF1610 DUF1936 DUF2116 DUF2180 DUF2387 DZR Elf1 GATA NinF NOB1_Zn_bind Ogr_Delta OrfB_Zn_ribbon PhnA_Zn_Ribbon Prim_Zn_Ribbon Ribosomal_L32p Ribosomal_L37ae Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD RRN7 Spt4 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 zf-C4_Topoisom zf-CHC2 zf-DHHC zf-dskA_traR zf-FPG_IleRS zf-GRF zf-NADH-PPase zf-RanBP zf-ribbon_3 zf-TFIIB zinc-ribbons_6 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 Zn-ribbon_8 Zn_ribbon_recom Zn_Tnp_IS1 Zn_Tnp_IS1595
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Curation and family details
|Seed source:||Pfam-B_1854 (release 3.0)|
|Number in seed:||27|
|Number in full:||10157|
|Average length of the domain:||39.50 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||11.65 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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