Nucleic Acids Research, 1989, Vol. 17, No. 12 4713-4730
© 1989
ENZYMOLOGY |
Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes
Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences 142782 Moscow region, USSR
*To whom correspondence should be addressed.
Received May 3, 1989. Accepted May 18, 1989.
In the course of systematic analysis of protein sequences containing the purine NTP-binding motif, a new superfamily was delineated which included 25 established or putative halicases of Escherichia coli, yeast, insects, mammals, pox- and herpesvirusea, a yeast mitochondriel plasmid and three groups of positive strand RNA viruses. These proteins contained 7 distinct highly conserved segments two of which corresponded to the "A" and "B" sites of the NTP–binding motif. Typical of the new superfamily was an abridged consensus for the "A" site, GxGKS/T, instead of the classical G/AxxxxGKS/T. Secondary structure predictions indicated that each of the conserved segments might constitute a separate structural unit centering at a ß–turn. All previously characterized mutations impairing the function of the yeast helicase RAD3 in DNA repair mapped to one of the conserved segments. A degree of similarity was revealed between the consensus pattern of conserved amino acid residues derived for the new superfamily and that of another recently described protein superfamily including a different set of prokaryotic, eukaryotic and viral (putative) helicases.
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J. W. George, E. P. Salazar, M. P. G. Vreeswijk, J. E. Lamerdin, J. T. Reardon, M. Z. Zdzienicka, A. Sancar, S. Kadkhodayan, R. S. Tebbs, L. H. F. Mullenders, et al. Restoration of Nucleotide Excision Repair in a Helicase-Deficient XPD Mutant from Intragenic Suppression by a Trichothiodystrophy Mutation Mol. Cell. Biol., November 1, 2001; 21(21): 7355 - 7365. [Abstract] [Full Text] [PDF]
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M. Ackermann and R. Padmanabhan De Novo Synthesis of RNA by the Dengue Virus RNA-dependent RNA Polymerase Exhibits Temperature Dependence at the Initiation but Not Elongation Phase J. Biol. Chem., October 19, 2001; 276(43): 39926 - 39937. [Abstract] [Full Text] [PDF]
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S. Tada, T. Kobayashi, A. Omori, Y. Kusa, N. Okumura, H. Kodaira, Y. Ishimi, M. Seki, and T. Enomoto Molecular cloning of a cDNA encoding mouse DNA helicase B, which has homology to Escherichia coli RecD protein, and identification of a mutation in the DNA helicase B from tsFT848 temperature-sensitive DNA replication mutant cells Nucleic Acids Res., September 15, 2001; 29(18): 3835 - 3840. [Abstract] [Full Text] [PDF]
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J. Rho, S. Choi, Y. R. Seong, J. Choi, and D.-S. Im The Arginine-1493 Residue in QRRGRTGR1493G Motif IV of the Hepatitis C Virus NS3 Helicase Domain Is Essential for NS3 Protein Methylation by the Protein Arginine Methyltransferase 1 J. Virol., September 1, 2001; 75(17): 8031 - 8044. [Abstract] [Full Text] [PDF]
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C.-L. Tai, W.-C. Pan, S.-H. Liaw, U.-C. Yang, L.-H. Hwang, and D.-S. Chen Structure-Based Mutational Analysis of the Hepatitis C Virus NS3 Helicase J. Virol., September 1, 2001; 75(17): 8289 - 8297. [Abstract] [Full Text] [PDF]
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A. C. Vlot, L. Neeleman, H. J. M. Linthorst, and J. F. Bol Role of the 3'-Untranslated Regions of Alfalfa Mosaic Virus RNAs in the Formation of a Transiently Expressed Replicase in Plants and in the Assembly of Virions J. Virol., July 15, 2001; 75(14): 6440 - 6449. [Abstract] [Full Text]
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P. Borowski, A. Niebuhr, O. Mueller, M. Bretner, K. Felczak, T. Kulikowski, and H. Schmitz Purification and Characterization of West Nile Virus Nucleoside Triphosphatase (NTPase)/Helicase: Evidence for Dissociation of the NTPase and Helicase Activities of the Enzyme J. Virol., April 1, 2001; 75(7): 3220 - 3229. [Abstract] [Full Text]
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A. Vindigni, A. Ochem, G. Triolo, and A. Falaschi Identification of human DNA helicase V with the far upstream element-binding protein Nucleic Acids Res., March 1, 2001; 29(5): 1061 - 1067. [Abstract] [Full Text] [PDF]
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K. Stasiak, M.-V. Demattei, B. A. Federici, and Y. Bigot Phylogenetic position of the Diadromus pulchellus ascovirus DNA polymerase among viruses with large double-stranded DNA genomes J. Gen. Virol., December 1, 2000; 81(12): 3059 - 3072. [Abstract] [Full Text]
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J. R. Walker, C. Hervas, J. D. Ross, A. Blinkova, M. J. Walbridge, E. J. Pumarega, M.-O. Park, and H. R. Neely Escherichia coli DNA Polymerase III tau - and gamma -Subunit Conserved Residues Required for Activity In Vivo and In Vitro J. Bacteriol., November 1, 2000; 182(21): 6106 - 6113. [Abstract] [Full Text]
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S. C. Chang, J.-C. Cheng, Y.-H. Kou, C.-H. Kao, C.-H. Chiu, H.-Y. Wu, and M.-F. Chang Roles of the AX4GKS and Arginine-Rich Motifs of Hepatitis C Virus RNA Helicase in ATP- and Viral RNA-Binding Activity J. Virol., October 15, 2000; 74(20): 9732 - 9737. [Abstract] [Full Text]
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A. D. Garcia, L. Aravind, E. V. Koonin, and B. Moss Bacterial-type DNA Holliday junction resolvases in eukaryotic viruses PNAS, July 5, 2000; (2000) 150238697. [Abstract] [Full Text]
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C. Paolini, A. Lahm, R. De Francesco, and P. Gallinari Mutational analysis of hepatitis C virus NS3-associated helicase J. Gen. Virol., July 1, 2000; 81(7): 1649 - 1658. [Abstract] [Full Text]
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D. W. Lee, K. Zhang, Z.-Q. Ning, E. H. Raabe, S. Tintner, R. Wieland, B. J. Wilkins, J. M. Kim, R. I. Blough, and R. J. Arceci Proliferation-associated SNF2-like Gene (PASG): A SNF2 Family Member Altered in Leukemia1 Cancer Res., July 1, 2000; 60(13): 3612 - 3622. [Abstract] [Full Text]
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H.-Y. Kang, E. Choi, S.-H. Bae, K.-H. Lee, B.-S. Gim, H.-D. Kim, C. Park, S. A. MacNeill, and Y.-S. Seo Genetic Analyses of Schizosaccharomyces pombe dna2+ Reveal That Dna2 Plays an Essential Role in Okazaki Fragment Metabolism Genetics, July 1, 2000; 155(3): 1055 - 1067. [Abstract] [Full Text]
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D. K. Bideshi and B. A. Federici DNA-independent ATPase activity of the Trichoplusia ni granulovirus DNA helicase J. Gen. Virol., June 1, 2000; 81(6): 1601 - 1604. [Abstract] [Full Text]
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A. A. Khromykh, P. L. Sedlak, and E. G. Westaway cis- and trans-Acting Elements in Flavivirus RNA Replication J. Virol., April 1, 2000; 74(7): 3253 - 3263. [Abstract] [Full Text]
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A. Shimamoto, K. Nishikawa, S. Kitao, and Y. Furuichi Human RecQ5{beta}, a large isomer of RecQ5 DNA helicase, localizes in the nucleoplasm and interacts with topoisomerases 3{alpha} and 3{beta} Nucleic Acids Res., April 1, 2000; 28(7): 1647 - 1655. [Abstract] [Full Text] [PDF]
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C. Czibener, J. L. La Torre, O. A. Muscio, R. A. Ugalde, and E. A. Scodeller Nucleotide sequence analysis of Triatoma virus shows that it is a member of a novel group of insect RNA viruses J. Gen. Virol., April 1, 2000; 81(4): 1149 - 1154. [Abstract] [Full Text]
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R. Yusof, S. Clum, M. Wetzel, H. M. K. Murthy, and R. Padmanabhan Purified NS2B/NS3 Serine Protease of Dengue Virus Type 2 Exhibits Cofactor NS2B Dependence for Cleavage of Substrates with Dibasic Amino Acids in Vitro J. Biol. Chem., March 31, 2000; 275(14): 9963 - 9969. [Abstract] [Full Text] [PDF]
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A. A. Kolykhalov, K. Mihalik, S. M. Feinstone, and C. M. Rice Hepatitis C Virus-Encoded Enzymatic Activities and Conserved RNA Elements in the 3' Nontranslated Region Are Essential for Virus Replication In Vivo J. Virol., February 15, 2000; 74(4): 2046 - 2051. [Abstract] [Full Text]
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L. B. Murata and M. S. Dodson The Herpes Simplex Virus Type 1 Origin-binding Protein. SEQUENCE-SPECIFIC ACTIVATION OF ADENOSINE TRIPHOSPHATASE ACTIVITY BY A DOUBLE-STRANDED DNA CONTAINING BOX I J. Biol. Chem., December 24, 1999; 274(52): 37079 - 37086. [Abstract] [Full Text] [PDF]
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S. You and R. Padmanabhan A Novel in Vitro Replication System for Dengue Virus. INITIATION OF RNA SYNTHESIS AT THE 3'-END OF EXOGENOUS VIRAL RNA TEMPLATES REQUIRES 5'- AND 3'-TERMINAL COMPLEMENTARY SEQUENCE MOTIFS OF THE VIRAL RNA J. Biol. Chem., November 19, 1999; 274(47): 33714 - 33722. [Abstract] [Full Text] [PDF]
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C. W. Grassmann, O. Isken, and S.-E. Behrens Assignment of the Multifunctional NS3 Protein of Bovine Viral Diarrhea Virus during RNA Replication: an In Vivo and In Vitro Study J. Virol., November 1, 1999; 73(11): 9196 - 9205. [Abstract] [Full Text] [PDF]
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I. R. Lehman and P. E. Boehmer Replication of Herpes Simplex Virus DNA J. Biol. Chem., October 1, 1999; 274(40): 28059 - 28062. [Full Text] [PDF]
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I. Iost, M. Dreyfus, and P. Linder Ded1p, a DEAD-box Protein Required for Translation Initiation in Saccharomyces cerevisiae, Is an RNA Helicase J. Biol. Chem., June 18, 1999; 274(25): 17677 - 17683. [Abstract] [Full Text] [PDF]
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