메뉴 건너뛰기




Volumn 13, Issue 8, 2004, Pages 2260-2269

Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease

Author keywords

dsDNA bacteriophage; Evolution; Gene organization; Homology detection; MEROPS; Prohead protease; Structure prediction

Indexed keywords

DOUBLE STRANDED DNA; HISTIDINE; PROTEINASE; SERINE;

EID: 3342951741     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04726004     Document Type: Article
Times cited : (60)

References (53)
  • 2
    • 0025943153 scopus 로고
    • Identification of the Escherichia coli sohB gene, a multicopy suppressor of the HtrA (DegP) null phenotype
    • Baird, L., Lipinska, B., Raina, S., and Georgopoulos, C. 1991. Identification of the Escherichia coli sohB gene, a multicopy suppressor of the HtrA (DegP) null phenotype. J. Bacteriol. 173: 5763-5770.
    • (1991) J. Bacteriol. , vol.173 , pp. 5763-5770
    • Baird, L.1    Lipinska, B.2    Raina, S.3    Georgopoulos, C.4
  • 3
    • 0035783060 scopus 로고    scopus 로고
    • The MEROPS database as a protease information system
    • Barrett, A.J., Rawlings, N.D., and O'Brien, E.A. 2001. The MEROPS database as a protease information system. J. Struct. Biol. 134: 95-102.
    • (2001) J. Struct. Biol. , vol.134 , pp. 95-102
    • Barrett, A.J.1    Rawlings, N.D.2    O'Brien, E.A.3
  • 5
    • 0035074910 scopus 로고    scopus 로고
    • The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis
    • Bujnicki, J.M. and Rychlewski, L. 2001. The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis. Virus Genes 22: 219-230.
    • (2001) Virus Genes , vol.22 , pp. 219-230
    • Bujnicki, J.M.1    Rychlewski, L.2
  • 6
    • 0033966457 scopus 로고    scopus 로고
    • The terminase enzyme from bacteriophage λ: A DNA-packaging machine
    • Catalano, C.E. 2000. The terminase enzyme from bacteriophage λ: A DNA-packaging machine. Cell. Mol. Life Sci. 57: 128-148.
    • (2000) Cell. Mol. Life Sci. , vol.57 , pp. 128-148
    • Catalano, C.E.1
  • 8
    • 0033178790 scopus 로고    scopus 로고
    • Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21
    • Desiere, F., Lucchini, S., and Brussow, H. 1999. Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21, Virology 260: 244-253.
    • (1999) Virology , vol.260 , pp. 244-253
    • Desiere, F.1    Lucchini, S.2    Brussow, H.3
  • 9
    • 0032712201 scopus 로고    scopus 로고
    • Scaffolding proteins and their role in viral assembly
    • Dokland, T. 1999. Scaffolding proteins and their role in viral assembly. Cell. Mol. Life Sci. 56: 580-603.
    • (1999) Cell. Mol. Life Sci. , vol.56 , pp. 580-603
    • Dokland, T.1
  • 11
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition metapredictor
    • Fischer, D. 2003. 3D-SHOTGUN: A novel, cooperative, fold-recognition metapredictor. Proteins 51: 434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 12
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski, K., Elofsson, A., Fischer, D., and Rychlewski, L. 2003. 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 13
    • 0029978730 scopus 로고    scopus 로고
    • Bacteriophage Mu head assembly
    • Grimaud, R. 1996. Bacteriophage Mu head assembly. Virology 217: 200-210.
    • (1996) Virology , vol.217 , pp. 200-210
    • Grimaud, R.1
  • 14
    • 0036856210 scopus 로고    scopus 로고
    • Euclidian space and grouping of biological objects
    • Grishin, V.N. and Grishin, N.V. 2002. Euclidian space and grouping of biological objects. Bioinformatics 18: 1523-1534.
    • (2002) Bioinformatics , vol.18 , pp. 1523-1534
    • Grishin, V.N.1    Grishin, N.V.2
  • 15
  • 16
    • 0031606857 scopus 로고    scopus 로고
    • Bacteriophage HK97 head assembly: A protein ballet
    • Hendrix, R.W. and Duda, R.L. 1998. Bacteriophage HK97 head assembly: A protein ballet. Adv. Virus Res. 50: 235-288.
    • (1998) Adv. Virus Res. , vol.50 , pp. 235-288
    • Hendrix, R.W.1    Duda, R.L.2
  • 17
    • 0030871678 scopus 로고    scopus 로고
    • Capsid assembly and DNA packaging in herpes simplex virus
    • Homa, F.L. and Brown, J.C. 1997. Capsid assembly and DNA packaging in herpes simplex virus. Rev. Med. Virol. 7: 107-122.
    • (1997) Rev. Med. Virol. , vol.7 , pp. 107-122
    • Homa, F.L.1    Brown, J.C.2
  • 18
    • 0036572959 scopus 로고    scopus 로고
    • Comparative analysis of the genomes of the temperate bacteriophages φ 11, φ 12 and φ 13 of Staphylococcus aureus 8325
    • Iandolo, J.J., Worrell, V., Groicher, K.H., Qian, Y., Tian, R., Kenton, S., Dorman, A., Ji, H., Lin, S., Loh, P., et al. 2002. Comparative analysis of the genomes of the temperate bacteriophages φ 11, φ 12 and φ 13 of Staphylococcus aureus 8325. Gene 289: 109-118.
    • (2002) Gene , vol.289 , pp. 109-118
    • Iandolo, J.J.1    Worrell, V.2    Groicher, K.H.3    Qian, Y.4    Tian, R.5    Kenton, S.6    Dorman, A.7    Ji, H.8    Lin, S.9    Loh, P.10
  • 19
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 20
    • 0035967516 scopus 로고    scopus 로고
    • Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease
    • Khayat, R., Batra, R., Massariol, M.J., Lagace, L., and Tong, L. 2001. Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease. Biochemistry 40: 6344-6351.
    • (2001) Biochemistry , vol.40 , pp. 6344-6351
    • Khayat, R.1    Batra, R.2    Massariol, M.J.3    Lagace, L.4    Tong, L.5
  • 21
    • 0036600834 scopus 로고    scopus 로고
    • Evolution of protein structures and functions
    • Kinch, L.N. and Grishin, N.V. 2002a. Evolution of protein structures and functions. Curr. Opin. Struct. Biol. 12: 400-408.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 400-408
    • Kinch, L.N.1    Grishin, N.V.2
  • 22
    • 0036643429 scopus 로고    scopus 로고
    • Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity
    • -. 2002b. Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity. Proteins 48: 75-84.
    • (2002) Proteins , vol.48 , pp. 75-84
  • 23
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24: 946-950.
    • (1991) J. Appl. Cryst. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 24
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology. Applications to protein modeling
    • Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235: 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 26
    • 0028844625 scopus 로고
    • Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes
    • Lubbers, M.W., Waterfield, N.R., Beresford, T.P., Le Page, R.W., and Jarvis, A.W. 1995. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl. Environ. Microbiol. 61: 4348-4356.
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 4348-4356
    • Lubbers, M.W.1    Waterfield, N.R.2    Beresford, T.P.3    Le Page, R.W.4    Jarvis, A.W.5
  • 27
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: A neural-network-based consensus predictor that improves fold recognition
    • Lundstrom, J., Rychlewski, L., Bujnicki, J., and Elofsson, A. 2001. Pcons: A neural-network-based consensus predictor that improves fold recognition. Protein Sci. 10: 2354-2362.
    • (2001) Protein Sci. , vol.10 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 28
    • 0034801343 scopus 로고    scopus 로고
    • The genome of archaeal prophage PsiM100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii
    • Luo, Y., Pfister, P., Leisinger, T., and Wasseffallen, A. 2001. The genome of archaeal prophage PsiM100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii. J. Bacteriol. 183: 5788-5792.
    • (2001) J. Bacteriol. , vol.183 , pp. 5788-5792
    • Luo, Y.1    Pfister, P.2    Leisinger, T.3    Wasseffallen, A.4
  • 29
    • 0031761964 scopus 로고    scopus 로고
    • Taxonomy of bacterial viruses: Establishment of tailed virus genera and the order Caudovirates
    • Maniloff, J. and Ackermann, H.W. 1998. Taxonomy of bacterial viruses: Establishment of tailed virus genera and the order Caudovirates. Arch. Virol. 143: 2051-2063.
    • (1998) Arch. Virol. , vol.143 , pp. 2051-2063
    • Maniloff, J.1    Ackermann, H.W.2
  • 31
    • 0037106323 scopus 로고    scopus 로고
    • Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases
    • Mitchell, M.S., Matsuzaki, S., Imai, S., and Rao, V.B. 2002. Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Res. 30: 4009-4021.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4009-4021
    • Mitchell, M.S.1    Matsuzaki, S.2    Imai, S.3    Rao, V.B.4
  • 32
    • 0036299014 scopus 로고    scopus 로고
    • Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus
    • Morgan, G.J., Hatfull, G.F., Casjens, S., and Hendrix, R.W. 2002. Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317: 337-359.
    • (2002) J. Mol. Biol. , vol.317 , pp. 337-359
    • Morgan, G.J.1    Hatfull, G.F.2    Casjens, S.3    Hendrix, R.W.4
  • 33
    • 0034766951 scopus 로고    scopus 로고
    • The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid
    • Newcomb, W.W., Juhas, R.M., Thomsen, D.R., Homa, F.L., Burch, A.D., Weller, S.K., and Brown, J.C. 2001. The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid. J. Virol. 75: 10923-10932.
    • (2001) J. Virol. , vol.75 , pp. 10923-10932
    • Newcomb, W.W.1    Juhas, R.M.2    Thomsen, D.R.3    Homa, F.L.4    Burch, A.D.5    Weller, S.K.6    Brown, J.C.7
  • 34
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 36
    • 0035254950 scopus 로고    scopus 로고
    • GGDEF domain is homologous to adenylyl cyclase
    • Pei, J. and Grishin, N.V. 2001. GGDEF domain is homologous to adenylyl cyclase. Proteins 42: 210-216.
    • (2001) Proteins , vol.42 , pp. 210-216
    • Pei, J.1    Grishin, N.V.2
  • 37
    • 0242515820 scopus 로고    scopus 로고
    • Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases
    • -. 2003. Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases. Protein Sci. 12: 1131-1135.
    • (2003) Protein Sci. , vol.12 , pp. 1131-1135
  • 38
    • 0037433034 scopus 로고    scopus 로고
    • PCMA: Fast and accurate multiple sequence alignment based on profile consistency
    • Pei, J., Sadreyev, R., and Grishin, N.V. 2003. PCMA: Fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19: 427-428.
    • (2003) Bioinformatics , vol.19 , pp. 427-428
    • Pei, J.1    Sadreyev, R.2    Grishin, N.V.3
  • 39
    • 0037689381 scopus 로고    scopus 로고
    • Complete sequence and comparative analysis of the genome of herpes B virus (Cercopithecine herpesvirus 1) from a rhesus monkey
    • Perelygina, L., Zhu, L., Zurkuhlen, H., Mills, R., Borodovsky, M., and Hilliard, J.K. 2003. Complete sequence and comparative analysis of the genome of herpes B virus (Cercopithecine herpesvirus 1) from a rhesus monkey. J. Virol. 77: 6167-6177.
    • (2003) J. Virol. , vol.77 , pp. 6167-6177
    • Perelygina, L.1    Zhu, L.2    Zurkuhlen, H.3    Mills, R.4    Borodovsky, M.5    Hilliard, J.K.6
  • 40
    • 0042389525 scopus 로고    scopus 로고
    • Point mutations in exon I of the herpes simplex virus putative terminase subunit, UL15, indicate that the most conserved residues are essential for cleavage and packaging
    • Przech, A.J., Yu, D., and Weller, S.K. 2003. Point mutations in exon I of the herpes simplex virus putative terminase subunit, UL15, indicate that the most conserved residues are essential for cleavage and packaging. J. Virol. 77: 9613-9621.
    • (2003) J. Virol. , vol.77 , pp. 9613-9621
    • Przech, A.J.1    Yu, D.2    Weller, S.K.3
  • 42
    • 0034711002 scopus 로고    scopus 로고
    • Functional consequences of the Kaposi's sarcoma-associated herpesvirus protease structure: Regulation of activity and dimerization by conserved structural elements
    • Reiling, K.K., Pray, T.R., Craik, C.S., and Stroud, R.M. 2000. Functional consequences of the Kaposi's sarcoma-associated herpesvirus protease structure: Regulation of activity and dimerization by conserved structural elements. Biochemistry 39: 12796-12803.
    • (2000) Biochemistry , vol.39 , pp. 12796-12803
    • Reiling, K.K.1    Pray, T.R.2    Craik, C.S.3    Stroud, R.M.4
  • 43
    • 0038468334 scopus 로고    scopus 로고
    • The herpes simplex virus type 1 alkaline nuclease and single-stranded DNA binding protein mediate strand exchange in vitro
    • Reuven, N.B., Staire, A.E., Myers, R.S., and Weller, S.K. 2003. The herpes simplex virus type 1 alkaline nuclease and single-stranded DNA binding protein mediate strand exchange in vitro. J. Virol. 77: 7425-7433.
    • (2003) J. Virol. , vol.77 , pp. 7425-7433
    • Reuven, N.B.1    Staire, A.E.2    Myers, R.S.3    Weller, S.K.4
  • 44
    • 0033928112 scopus 로고    scopus 로고
    • Evidence for controlled incorporation of herpes simplex virus type 1 UL26 protease into capsids
    • Sheaffer, A.K., Newcomb, W.W., Brown, J.C., Gao, M., Weller, S.K., and Tenney, D.J. 2000. Evidence for controlled incorporation of herpes simplex virus type 1 UL26 protease into capsids. J. Virol. 74: 6838-6848.
    • (2000) J. Virol. , vol.74 , pp. 6838-6848
    • Sheaffer, A.K.1    Newcomb, W.W.2    Brown, J.C.3    Gao, M.4    Weller, S.K.5    Tenney, D.J.6
  • 45
    • 0027522436 scopus 로고
    • Sequence analysis of the phage 21 genes for prohead assembly and head completion
    • Smith, M.P., and Feiss, M. 1993. Sequence analysis of the phage 21 genes for prohead assembly and head completion. Gene 126: 1-7.
    • (1993) Gene , vol.126 , pp. 1-7
    • Smith, M.P.1    Feiss, M.2
  • 46
    • 0033562324 scopus 로고    scopus 로고
    • The complete genome sequence of the Streptomyces temperate phage straight phiC31: Evolutionary relationships to other viruses
    • Smith, M.C., Burns, R.N., Wilson, S.E., and Gregory, M.A. 1999. The complete genome sequence of the Streptomyces temperate phage straight phiC31: Evolutionary relationships to other viruses. Nucleic Acids Res. 27: 2145-2155.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2145-2155
    • Smith, M.C.1    Burns, R.N.2    Wilson, S.E.3    Gregory, M.A.4
  • 48
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 49
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 50
    • 0036882392 scopus 로고    scopus 로고
    • Viral proteases
    • Tong, L. 2002. Viral proteases. Chem. Rev. 102: 4609-4626.
    • (2002) Chem. Rev. , vol.102 , pp. 4609-4626
    • Tong, L.1
  • 51
    • 0029793554 scopus 로고    scopus 로고
    • A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease
    • Tong, L., Qian, C., Massariol, M.J., Bonneau, P.R., Cordingley, M.G., and Lagace, L. 1996. A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature 383: 272-275.
    • (1996) Nature , vol.383 , pp. 272-275
    • Tong, L.1    Qian, C.2    Massariol, M.J.3    Bonneau, P.R.4    Cordingley, M.G.5    Lagace, L.6
  • 53
    • 0030691115 scopus 로고    scopus 로고
    • The structure of CIpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis
    • Wang, J., Hartling, J.A., and Flanagan, J.M. 1997. The structure of CIpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis. Cell 91: 447-456.
    • (1997) Cell , vol.91 , pp. 447-456
    • Wang, J.1    Hartling, J.A.2    Flanagan, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.