Summary: Toprim domain
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Toprim domain Provide feedback
This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1]. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity [1]. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division [2]. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases [4]. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Literature references
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Aravind L, Leipe DD, Koonin EV; , Nucleic Acids Res 1998;26:4205-4213.: Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. PUBMED:9722641 EPMC:9722641
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Szafranski P, Smith CL, Cantor CR; , Biochim Biophys Acta 1997;1352:243-248.: Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. PUBMED:9224947 EPMC:9224947
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Versalovic J, Lupski JR; , Gene 1993;136:281-286.: The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. PUBMED:8294018 EPMC:8294018
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Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P; , Nature 1997;386:414-417.: An atypical topoisomerase II from Archaea with implications for meiotic recombination. PUBMED:9121560 EPMC:9121560
Internal database links
SCOOP: | RecR Toprim_2 Toprim_3 Toprim_4 |
Similarity to PfamA using HHSearch: | Toprim_2 Toprim_3 Toprim_4 |
External database links
HOMSTRAD: | Toprim |
SCOP: | 1ecl |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006171
The Toprim (topoisomerase-primase) domain is a structurally conserved domain of ~100 amino acids that is found in bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, type IA and type II topoisomerases, bacterial and archaeal nucleases of the OLD family and bacterial DNA repair proteins of the RecR/M family. The Toprim domain can be found alone or in combination with several other domains, such as the ASM domain, the superfamily 2 helicase domain, the superfamily 3 helicase domain, the DnaB interaction domain, the C4 'little finger' domain, the CHC2 zinc finger, the ATPase domain of the HSP90-gyrase-histidine kinase superfamily, the S5 domain, the SET domain, the helix-hairpin-helix (HhH) DNA-binding domain, the mobilisation (MOB) domain or the ATPase domain of the ABC transporter/SMC superfamily. The Toprim domain is a catalytic domain involved in DNA strand breakage and rejoining [PUBMED:9722641].
The Toprim domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). Both motifs are preceded by conserved hydrophobic regions predicted to form beta-strands. The glutamate residue is probably involved in catalysis, whereas the DxD motif is involved in the co-ordination of Mg(2++) that is required for the activity of all Toprim-containing enzymes. The Toprim domain has a compact alpha/beta fold, with four conserved strands and three helices; with the exception of the second helix and the C-terminal strands, each of these elements contains positions that are highly conserved. The Toprim domain contains three regions that can accommodate variable sized inserts, which are particularly prominent in the topoisomerases [PUBMED:9722641, PUBMED:16077031, PUBMED:19596812].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Toprim-like (CL0413), which has the following description:
This is families that have a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1].
The clan contains the following 7 members:
DUF2220 DUF2399 DUF3854 Toprim Toprim_2 Toprim_3 Toprim_4Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (133) |
Full (27720) |
Representative proteomes | UniProt (136712) |
NCBI (238514) |
Meta (8313) |
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RP15 (3815) |
RP35 (13421) |
RP55 (26894) |
RP75 (46513) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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Seed (133) |
Full (27720) |
Representative proteomes | UniProt (136712) |
NCBI (238514) |
Meta (8313) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (3815) |
RP35 (13421) |
RP55 (26894) |
RP75 (46513) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_500 (release 4.2) |
Previous IDs: | Primase; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 133 |
Number in full: | 27720 |
Average length of the domain: | 119.20 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 15.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 104 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 8 interactions for this family. More...
DNA_gyraseB_C DNA_topoisoIV Topoisom_bac DNA_gyraseB_C Toprim DEAD DNA_topoisoIV Topoisom_bacStructures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Toprim domain has been found. There are 263 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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