|SMART accession number:||SM00493|
|Description:||topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins|
|Interpro abstract (IPR006171):|
This entry represents the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins [(PUBMED:9722641)]. The Toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.
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- Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with TOPRIM domain is also avaliable.
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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
- Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Aravind L, Leipe DD, Koonin EV
- Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
- Nucleic Acids Res. 1998; 26: 4205-13
- Display abstract
Iterative profile searches and structural modeling show that 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 contain a common domain, designated Toprim (topoisomerase-primase) domain. The domain consists of approximately 100 amino acids and has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). Examination of the structure of Topo IA and Topo II and modeling of the Toprim domains of the primases reveal a compact beta/alpha fold, with the conserved negatively charged residues juxtaposed, and inserts seen in Topo IA and Topo II. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand rejoining by topoisomerases and as a general acid in strand cleavage by topoisomerases and nucleases. The role of this glutamate in catalysis is supported by site-directed mutagenesis data on primases and Topo IA. The DxD motif may coordinate Mg2+that is required for the activity of all Toprim-containing enzymes. The common ancestor of all life forms could encode a prototype Toprim enzyme that might have had both nucleotidyl transferase and polynucleotide cleaving activity.
- Szafranski P, Smith CL, Cantor CR
- Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase.
- Biochim Biophys Acta. 1997; 1352: 243-8
- Display abstract
The dnaG gene coding for primase, a key enzyme in DNA replication, has been isolated from chromosomal DNA of the soil bacterium Pseudomonas putida. It maps within the putative MMS operon, between the rpsU and rpoD genes. Comparison of the deduced amino acid sequence of P. putida DnaG with sequences of other known bacterial primases reveals the presence of a possible regulatory region which would be unique to pseudomonads. The analysis of nucleotide sequence suggests that stable folding of the dnaG mRNA may significantly contribute to the low level of its expression within a cell.
- Lima CD, Wang JC, Mondragon A
- Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I.
- Nature. 1994; 367: 138-46
- Display abstract
The three-dimensional structure of the 67K amino-terminal fragment of Escherichia coli DNA topoisomerase I has been determined to 2.2 A resolution. The polypeptide folds in an unusual way to give four distinct domains enclosing a hole large enough to accommodate a double-stranded DNA. The active-site tyrosyl residue, which is involved in the transient breakage of a DNA strand and the formation of a covalent enzyme-DNA intermediate, is present at the interface of two domains. The structure suggests a plausible mechanism by which E. coli DNA topoisomerase I and other members of the same DNA topoisomerase subfamily could catalyse the passage of one DNA strand through a transient break in another strand.
- Metabolism (metabolic pathways involving proteins which contain this domain)
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% proteins involved KEGG pathway ID Description 98.35 map03030 DNA replication 0.83 map00740 Riboflavin metabolism 0.28 map02060 Phosphotransferase system (PTS) 0.28 map00730 Thiamine metabolism 0.28 map00230 Purine metabolism
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with TOPRIM domain which could be assigned to a KEGG orthologous group, and not all proteins containing TOPRIM domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
- Structure (3D structures containing this domain)
3D Structures of TOPRIM domains in PDB
PDB code Main view Title 1cy0 Complex of e.coli dna topoisomerase i with 3'-5'-adenosine diphosphate 1cy1 Complex of e.coli dna topoisomerase i with 5'ptptpt 1cy2 Complex of e.coli dna topoisomerase i with tptptp3' 1cy4 Complex of e.coli dna topoisomerase i with 5'ptptptp3' 1cy6 Complex of e.coli dna topoisomerase i with 3' thymidine monophosphate 1cy7 Complex of e.coli dna topoisomerase i with 5'-thymidine monophosphate 1cy8 Complex of e.coli dna topoisomerase i with 5'-thymidine monophosphate and 3'-thymidine monophosphate 1d6m Crystal structure of e. coli dna topoisomerase iii 1dd9 Structure of the dnag catalytic core 1dde Structure of the dnag catalytic core 1ecl Amino terminal 67kda domain of escherichia coli dna topoisomerase i (residues 2-590 of mature protein) cloning artifact adds two residues to the amino-terminus which were not observed in the experimental electron density (gly-2, ser-1). 1eqn E.coli primase catalytic core 1gku Reverse gyrase from archaeoglobus fulgidus 1gl9 Archaeoglobus fulgidus reverse gyrase complexed with adpnp 1i7d Noncovalent complex of e.coli dna topoisomerase iii with an 8-base single-stranded dna oligonucleotide 1mw8 Crystal structure of a complex between h365r mutant of 67 kda n-terminal fragment of e. coli dna topoisomerase i and 5'-acttcgggatg-3' 1mw9 Crystal structure of h365r mutant of 67 kda n-terminal fragment of e. coli dna topoisomerase i 1nui Crystal structure of the primase fragment of bacteriophage t7 primase-helicase protein 1q57 The crystal structure of the bifunctional primase-helicase of bacteriophage t7 1t6t Putative protein from aquifex aeolicus 1vdd Crystal structure of recombinational repair protein recr 2au3 Crystal structure of the aquifex aeolicus primase (zinc binding and rna polymerase domains) 2fcj Structure of small toprim domain protein from bacillus stearothermophilus. 2gai Structure of full length topoisomerase i from thermotoga maritima in triclinic crystal form 2gaj Structure of full length topoisomerase i from thermotoga maritima in monoclinic crystal form 2i5r Structure of small toprim domain-containing protein from b. stearothermophilus in complex with mg2+ 2o19 Structure of e. coli topoisomersae iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol at ph 5.5 2o54 Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol at ph 7.0 2o59 Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol ph 8.0 2o5c Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glucose ph 5.5 2o5e Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glucose ph 7.0 2v1c Crystal structure and mutational study of recor provide insight into its role in dna repair 3b39 Structure of the dnag primase catalytic domain bound to ssdna
- Links (links to other resources describing this domain)
PFAM Primase INTERPRO IPR006171