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{
"metadata": {
"accession": "IPR006343",
"entry_id": null,
"type": "domain",
"go_terms": null,
"source_database": "interpro",
"member_databases": {
"pfam": {
"PF07261": "Replication initiation and membrane attachment"
},
"ncbifam": {
"TIGR01446": "DnaD domain protein"
}
},
"integrated": null,
"hierarchy": {
"accession": "IPR006343",
"name": "DnaB/C, C-terminal domain",
"type": "Domain",
"children": []
},
"name": {
"name": "DnaB/C, C-terminal domain",
"short": "DnaB/C_C"
},
"description": [
{
"text": "<p>This entry describes the C-terminal domain in DnaB, DnaD and related bacterial proteins. This domain is α-helical.</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>DnaB is a key component of the bacterial DNA replication machinery, involved in both initiation and replication restart. It functions in coordination with DnaI to assist in loading the replicative helicase DnaC onto single-stranded DNA. During initiation at the chromosomal origin of replication, oriC, DnaB acts downstream of DnaA and requires the prior action of DnaD. Beyond its role at oriC, DnaB is also a component of the replication restart primosome, enabling helicase reloading at alternative chromosomal sites, possibly through a PriA-independent pathway. DnaB and DnaD work cooperatively to enable DnaB access to single-stranded DNA, and they are essential for helicase loading at the oriN of the repN plasmid. DnaB is believed to mediate replication initiation at the inner face of the cell membrane and is critical for anchoring the origin region of both chromosomal DNA and plasmids to the membrane. It binds weakly to single-stranded DNA, shows a preference for double-stranded DNA and replication fork-like substrates, and remodels DNA by laterally compacting supercoiled and linear plasmid DNA, forming bead-like structures along double-stranded DNA. Together with DnaD, DnaB forms bipolar complexes on plasmid DNA, highlighting its central role in DNA replication and structural organisation [[cite:PUB00160774], [cite:PUB00160776], [cite:PUB00160775]].</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA [[cite:PUB00009584]]. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria [[cite:PUB00009584]]. DnaD consists of two domains with distinct activities: an N-terminal domain with oligomerisation activity and a C-terminal domain with DNA-binding activity and a second DNA-induced oligomerisation activity [[cite:PUB00085025]].</p>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00009584": {
"PMID": 11679082,
"ISBN": null,
"volume": "42",
"issue": "1",
"year": 2001,
"title": "DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome.",
"URL": null,
"raw_pages": "245-55",
"medline_journal": "Mol Microbiol",
"ISO_journal": "Mol. Microbiol.",
"authors": [
"Bruand C",
"Farache M",
"McGovern S",
"Ehrlich SD",
"Polard P."
],
"DOI_URL": "http://dx.doi.org/10.1046/j.1365-2958.2001.02631.x"
},
"PUB00085025": {
"PMID": 16677303,
"ISBN": null,
"volume": "60",
"issue": "4",
"year": 2006,
"title": "The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains.",
"URL": null,
"raw_pages": "917-24",
"medline_journal": "Mol Microbiol",
"ISO_journal": "Mol. Microbiol.",
"authors": [
"Carneiro MJ",
"Zhang W",
"Ioannou C",
"Scott DJ",
"Allen S",
"Roberts CJ",
"Soultanas P."
],
"DOI_URL": "https://doi.org/10.1111/j.1365-2958.2006.05152.x"
},
"PUB00160774": {
"PMID": 12718886,
"ISBN": null,
"volume": "11",
"issue": "4",
"year": 2003,
"title": "A two-protein strategy for the functional loading of a cellular replicative DNA helicase.",
"URL": null,
"raw_pages": "1009-20",
"medline_journal": "Mol Cell",
"ISO_journal": "Mol Cell",
"authors": [
"Velten M",
"McGovern S",
"Marsin S",
"Ehrlich SD",
"Noirot P",
"Polard P."
],
"DOI_URL": "https://doi.org/10.1016/s1097-2765(03)00130-8"
},
"PUB00160775": {
"PMID": 15186423,
"ISBN": null,
"volume": "52",
"issue": "6",
"year": 2004,
"title": "Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis.",
"URL": null,
"raw_pages": "1757-67",
"medline_journal": "Mol Microbiol",
"ISO_journal": "Mol Microbiol",
"authors": [
"Rokop ME",
"Auchtung JM",
"Grossman AD."
],
"DOI_URL": "https://doi.org/10.1111/j.1365-2958.2004.04091.x"
},
"PUB00160776": {
"PMID": 19968790,
"ISBN": null,
"volume": "75",
"issue": "2",
"year": 2010,
"title": "Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo.",
"URL": null,
"raw_pages": "452-61",
"medline_journal": "Mol Microbiol",
"ISO_journal": "Mol Microbiol",
"authors": [
"Smits WK",
"Goranov AI",
"Grossman AD."
],
"DOI_URL": "https://doi.org/10.1111/j.1365-2958.2009.06999.x"
}
},
"set_info": null,
"overlaps_with": [
{
"accession": "IPR034829",
"name": "DnaD-like domain superfamily",
"type": "homologous_superfamily"
}
],
"counters": {
"subfamilies": 0,
"domain_architectures": 32,
"interactions": 0,
"matches": 13085,
"pathways": 0,
"proteins": 11734,
"proteomes": 3366,
"sets": 0,
"structural_models": {
"alphafold": 9223,
"bfvd": 12
},
"structures": 3,
"taxa": 6231
},
"entry_annotations": {
"alignment:seed": 140,
"alignment:full": 4154
},
"cross_references": {},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": {
"accession": "2i5u",
"name": "Crystal structure of DnaD domain protein from Enterococcus faecalis. Structural genomics target APC85179"
}
}
}
