{"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,"updated":false}],"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"}}}