TOPRIM

• SMART accession number: SM00493
• Description: topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins
• Interpro abstract (IPR006154):

  The toprim (topoisomerase-primase) domain is a conserved region from DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins. The fold of the TOPRIM domain resembles a Rossman-like nucleotide binding fold, with a central beta-sheet formed by 4 parallel beta-strands flanked by 3 alpha-helices. Only 5 residues are conserved across all TOPRIM domain, 2 of these are glycines which may play a structural role, the other 3 are acidic residues that are present in 2 conserved sequence motifs. These may have a metal binding function (PUBMED:10873470)

  The TOPRIM domain may form a shallow groove on these molecules and play a role in the binding of double-helical DNA/RNA hybrids.

• GO process: DNA metabolic process (GO:0006259)
• GO function: nucleic acid binding (GO:0003676)

There are 3269 TOPRIM domains in 3269 proteins in SMART's nrdb database.

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

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

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

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)

% 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	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: IPR006154