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{
"metadata": {
"accession": "PS51194",
"entry_id": null,
"type": "domain",
"go_terms": null,
"source_database": "profile",
"member_databases": null,
"integrated": "IPR001650",
"hierarchy": null,
"name": {
"name": "Superfamilies 1 and 2 helicase C-terminal domain profile",
"short": "HELICASE_CTER"
},
"description": [
{
"text": "<p>Helicases have been classified in 5 superfamilies (SF1-SF5) [1]. All of the\nproteins bind ATP and, consequently, all of them carry the classical Walker A\n(phosphate-binding loop or P-loop) and Walker B\n(Mg2+-binding aspartic acid) motifs [1]. For the two largest groups, commonly\nreferred to as SF1 and SF2, a total of seven characteristic motifs has been\nidentified [[cite:PUB00004361]]. These two superfamilies encompass a large number of DNA and\nRNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be\nactive as monomers or dimers. RNA and DNA helicases are considered to be\nenzymes that catalyze the separation of double-stranded nucleic acids in an\nenergy-dependent manner [[cite:PUB00033619]].\n\nThe various structures of SF1 and SF2 helicases present a common core with two\nalpha-beta RecA-like domains (see for example {PDB:1FUU}) [[cite:PUB00033619]][[cite:PUB00025034]]. The\nstructural homology with the RecA recombination protein covers the five\ncontiguous parallel beta strands and the tandem alpha helices. ATP binds to\nthe amino proximal alpha-beta domain, where the Walker A (motif I) and Walker\nB (motif II) are found. The N-terminal domain also contains motif III (S-A-T)\nwhich was proposed to participate in linking ATPase and helicase activities.\nThe carboxy-terminal alpha-beta domain is structurally very similar to the\nproximal one even though it is bereft of an ATP-binding site, suggesting that\nit may have originally arisen through gene duplication of the first one.\n\nSome members of helicase superfamilies 1 and 2 are listed below:\n\n - DEAD-box RNA helicases. The prototype of DEAD-box\n proteins is the translation initiation factor eIF4A. The eIF4A protein is\n an RNA-dependent ATPase which functions together with eIF4B as an RNA\n helicases [[cite:PUB00033620]].\n - DEAH-box RNA helicases. Mainly pre-mRNA-splicing factor\n ATP-dependent RNA helicases [[cite:PUB00033620]].\n - Eukaryotic DNA repair helicase RAD3/ERCC-2, an ATP-dependent 5'-3' DNA\n helicase involved in nucleotide excision repair of UV-damaged DNA.\n - Eukaryotic TFIIH basal transcription factor complex helicase XPB subunit.\n An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH\n basal transcription factor, involved in nucleotide excision repair (NER) of\n DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.\n It acts by opening DNA either around the RNA transcription start site or\n the DNA.\n - Eukaryotic ATP-dependent DNA helicase Q. A DNA helicase that may play a\n role in the repair of DNA that is damaged by ultraviolet light or other\n mutagens.\n - Eukaryotic ATP-dependent helicase SNF2/RAD54. A group of ATP-dependent\n remodelling factors frequently found associated with histone deacetylases.\n - Bacterial and eukaryotic antiviral SKI2-like helicase. SKI2 has a role in\n the 3'-mRNA degradation pathway. It represses dsRNA virus propagation by\n specifically blocking translation of viral mRNAs, perhaps recognizing the\n absence of CAP or poly(A).\n - Bacterial DNA-damage-inducible protein G (DinG). A probable helicase\n involved in DNA repair and perhaps also replication.\n - Bacterial primosomal protein N' (PriA). PriA protein is one of seven\n proteins that make up the restart primosome, an apparatus that promotes\n assembly of replisomes at recombination intermediates and stalled\n replication forks.\n - Bacterial ATP-dependent DNA helicase recG. It has a critical role in\n recombination and DNA repair. It helps process Holliday junction\n intermediates to mature products by catalyzing branch migration. It has a\n DNA unwinding activity characteristic of a DNA helicase with a 3' to 5'\n polarity.\n - ssRNA positive-strand flaviviruses and potyviruses RNA helicase.\n - dsDNA viruses early transcription factor 70 kDa subunit.\n - dsDNA viruses nucleoside triphosphatase I (NPH I) protein. It serves two\n roles in transcription; it acts in concert with viral termination\n factor/capping enzyme to catalyze release of UUUUUNU-containing nascent RNA\n from the elongation complex, and it acts by itself as a polymerase\n elongation factor to facilitate readthrough of intrinsic pause sites.\n - Poxviruses transcript release DNA helicase. It prevents virus-induced\n breakdown of RNA. It acts as a negative transcription elongation factor. It\n is involved in an ATP-dependent manner in release of nascent RNA.\n\nTo recognize helicase Superfamilies 1 and 2 we have developed two profiles.\nThe first one recognizes all classical SF1 and SF2 helicases except bacterial\nDinG protein and eukaryotic Rad3 which belong to the same subfamily and which\ndiffer from other SF1-SF2 helicases by the presence of a large insert after\nthe Walker A [[cite:PUB00033621]]. Our second profile recognizes specifically this subfamily.</p>",
"llm": false,
"checked": false,
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}
],
"wikipedia": null,
"literature": {
"PUB00033620": {
"PMID": 11545728,
"ISBN": null,
"volume": "8",
"issue": "2",
"year": 2001,
"title": "DExD/H box RNA helicases: from generic motors to specific dissociation functions.",
"URL": null,
"raw_pages": "251-62",
"medline_journal": "Mol Cell",
"ISO_journal": "Mol. Cell",
"authors": [
"Tanner NK",
"Linder P."
],
"DOI_URL": "http://dx.doi.org/10.1016/S1097-2765(01)00329-X"
},
"PUB00004361": {
"PMID": 2546125,
"ISBN": null,
"volume": "17",
"issue": "12",
"year": 1989,
"title": "Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes.",
"URL": null,
"raw_pages": "4713-30",
"medline_journal": "Nucleic Acids Res",
"ISO_journal": "Nucleic Acids Res.",
"authors": [
"Gorbalenya AE",
"Koonin EV",
"Donchenko AP",
"Blinov VM."
],
"DOI_URL": "http://dx.doi.org/10.1093/nar/17.12.4713"
},
"PUB00033621": {
"PMID": 8385320,
"ISBN": null,
"volume": "21",
"issue": "6",
"year": 1993,
"title": "Escherichia coli dinG gene encodes a putative DNA helicase related to a group of eukaryotic helicases including Rad3 protein.",
"URL": null,
"raw_pages": "1497",
"medline_journal": "Nucleic Acids Res",
"ISO_journal": "Nucleic Acids Res.",
"authors": [
"Koonin EV."
],
"DOI_URL": "http://dx.doi.org/10.1093/nar/21.6.1497"
},
"PUB00025034": {
"PMID": 11087862,
"ISBN": null,
"volume": "97",
"issue": "24",
"year": 2000,
"title": "Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase.",
"URL": null,
"raw_pages": "13080-5",
"medline_journal": "Proc Natl Acad Sci U S A",
"ISO_journal": "Proc. Natl. Acad. Sci. U.S.A.",
"authors": [
"Caruthers JM",
"Johnson ER",
"McKay DB."
],
"DOI_URL": "http://dx.doi.org/10.1073/pnas.97.24.13080"
},
"PUB00033619": {
"PMID": 11839499,
"ISBN": null,
"volume": "12",
"issue": "1",
"year": 2002,
"title": "Helicase structure and mechanism.",
"URL": null,
"raw_pages": "123-33",
"medline_journal": "Curr Opin Struct Biol",
"ISO_journal": "Curr. Opin. Struct. Biol.",
"authors": [
"Caruthers JM",
"McKay DB."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0959-440X(02)00298-1"
}
},
"set_info": null,
"overlaps_with": null,
"counters": {
"subfamilies": 0,
"domain_architectures": 0,
"interactions": 0,
"matches": 893378,
"pathways": 0,
"proteins": 887857,
"proteomes": 22796,
"sets": 0,
"structural_models": {
"alphafold": 584321,
"bfvd": 182
},
"structures": 1237,
"taxa": 49836
},
"entry_annotations": {},
"cross_references": {},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": {
"accession": "1fuk",
"name": "CRYSTAL STRUCTURE OF THE CARBOXY TERMINAL DOMAIN OF YEAST EIF4A"
}
}
}
