-
1
-
-
0003422388
-
-
W.H. Freeman & Co., NY
-
Lodish,H., Berk,A., Zipursky,S.L., Matsudaira,P., Baltimore,D. and Darnell,J.E. (1999) Molecular Cell Biology. W.H. Freeman & Co., NY.
-
(1999)
Molecular Cell Biology
-
-
Lodish, H.1
Berk, A.2
Zipursky, S.L.3
Matsudaira, P.4
Baltimore, D.5
Darnell, J.E.6
-
3
-
-
0025815855
-
Protein-priming of DNA replication
-
Salas,M. (1991) Protein-priming of DNA replication. Annu. Rev. Biochem., 60, 39-71.
-
(1991)
Annu. Rev. Biochem.
, vol.60
, pp. 39-71
-
-
Salas, M.1
-
4
-
-
0029908732
-
Change of a catalytic reaction carried out by a DNA replication protein
-
Noirot-Gros,M.F. and Ehrlich,S.D. (1996) Change of a catalytic reaction carried out by a DNA replication protein. Science, 274, 777-780.
-
(1996)
Science
, vol.274
, pp. 777-780
-
-
Noirot-Gros, M.F.1
Ehrlich, S.D.2
-
5
-
-
0026748738
-
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria
-
Ilyina,T.V. and Koonin,E.V. (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res., 20, 3279-3285.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 3279-3285
-
-
Ilyina, T.V.1
Koonin, E.V.2
-
6
-
-
0032530488
-
Toprim - A conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins
-
Aravind,L., Leipe,D.D. and Koonin,E.V. (1998) Toprim - a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res., 26 4205-4213.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4205-4213
-
-
Aravind, L.1
Leipe, D.D.2
Koonin, E.V.3
-
7
-
-
0034737468
-
Structure of the RNA polymerase domain of E. coli primase
-
Keck,J.L., Roche,D.D., Lynch,A.S. and Berger,J.M. (2000) Structure of the RNA polymerase domain of E. coli primase. Science, 287, 2482-2486.
-
(2000)
Science
, vol.287
, pp. 2482-2486
-
-
Keck, J.L.1
Roche, D.D.2
Lynch, A.S.3
Berger, J.M.4
-
8
-
-
0035169689
-
Crystal structure of a DNA-dependent RNA polymerase (DNA primase)
-
Augustin,M.A., Huber,R. and Kaiser,J.T. (2001) Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Nature Struct. Biol., 8, 57-61.
-
(2001)
Nature Struct. Biol.
, vol.8
, pp. 57-61
-
-
Augustin, M.A.1
Huber, R.2
Kaiser, J.T.3
-
9
-
-
0036601353
-
Trends in protein evolution inferred from sequence and structure analysis
-
Aravind,L., Mazumder,R., Vasudevan,S. and Koonin,E.V. (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol., 12, 392-399.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 392-399
-
-
Aravind, L.1
Mazumder, R.2
Vasudevan, S.3
Koonin, E.V.4
-
10
-
-
0021770887
-
Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses
-
Kamer,G. and Argos,P. (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res., 12, 7269-7282.
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 7269-7282
-
-
Kamer, G.1
Argos, P.2
-
11
-
-
0024784519
-
Identification of four conserved motifs among the RNA-dependent polymerase encoding elements
-
Poch,O., Sauvaget,I., Delarue,M. and Tordo,N. (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J., 8, 3867-3874.
-
(1989)
EMBO J.
, vol.8
, pp. 3867-3874
-
-
Poch, O.1
Sauvaget, I.2
Delarue, M.3
Tordo, N.4
-
12
-
-
0025040632
-
An attempt to unify the structure of polymerases
-
Delarue,M., Poch,O., Tordo,N., Moras,D. and Argos,P. (1990) An attempt to unify the structure of polymerases. Protein Eng., 3, 461-467.
-
(1990)
Protein Eng.
, vol.3
, pp. 461-467
-
-
Delarue, M.1
Poch, O.2
Tordo, N.3
Moras, D.4
Argos, P.5
-
13
-
-
0032104477
-
How far divergent evolution goes in proteins
-
Murzin,A.G. (1998) How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol., 8, 380-387.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 380-387
-
-
Murzin, A.G.1
-
14
-
-
0035254950
-
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
-
15
-
-
0037079680
-
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
-
Makarova,K.S., Aravind,L., Grishin,N.V., Rogozin,I.B. and Koonin,E.V. (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30, 482-496.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 482-496
-
-
Makarova, K.S.1
Aravind, L.2
Grishin, N.V.3
Rogozin, I.B.4
Koonin, E.V.5
-
16
-
-
0035941229
-
Eukaryotic DNA polymerases: Proposal for a revised nomenclature
-
Burgers,P.M., Koonin,E.V., Bruford,E., Blanco,L., Burtis,K.C., Christman,M.F., Copeland,W.C., Friedberg,E.C., Hanaoka,F., Hinkle,D.C. et al. (2001) Eukaryotic DNA polymerases: Proposal for a revised nomenclature. J. Biol. Chem., 276, 43487-43490.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 43487-43490
-
-
Burgers, P.M.1
Koonin, E.V.2
Bruford, E.3
Blanco, L.4
Burtis, K.C.5
Christman, M.F.6
Copeland, W.C.7
Friedberg, E.C.8
Hanaoka, F.9
Hinkle, D.C.10
-
17
-
-
0027217643
-
Compilation, alignment, and phylogenetic relationships of DNA polymerases
-
Braithwaite,D.K. and Ito,J. (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res., 21, 787-802.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 787-802
-
-
Braithwaite, D.K.1
Ito, J.2
-
18
-
-
0033199713
-
Did DNA replication evolve twice independently?
-
Leipe,D.D., Aravind,L. and Koonin,E.V. (1999) Did DNA replication evolve twice independently? Nucleic Acids Res., 27, 3389-3401.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 3389-3401
-
-
Leipe, D.D.1
Aravind, L.2
Koonin, E.V.3
-
19
-
-
0032810166
-
Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins
-
Forterre,P. (1999) Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol., 33, 457-465.
-
(1999)
Mol. Microbiol.
, vol.33
, pp. 457-465
-
-
Forterre, P.1
-
20
-
-
0142217167
-
An exosome-like complex in Sulfolobus solfataricus
-
Evguenieva-Hackenburg,E., Walter.P., Hochleitner,E., Lottspeich,F. and Klug,G. (2003) An exosome-like complex in Sulfolobus solfataricus. EMBO Rep., 4, 889-893.
-
(2003)
EMBO Rep.
, vol.4
, pp. 889-893
-
-
Evguenieva-Hackenburg, E.1
Walter, P.2
Hochleitner, E.3
Lottspeich, F.4
Klug, G.5
-
21
-
-
0033759217
-
Bacterial homologs of the small subunit of eukaryotic DNA primase
-
Koonin,E.V., Wolf,Y.I., Kondrashov,A.S. and Aravind,L. (2000) Bacterial homologs of the small subunit of eukaryotic DNA primase. J. Mol. Microbiol. Biotechnol., 2, 509-512.
-
(2000)
J. Mol. Microbiol. Biotechnol.
, vol.2
, pp. 509-512
-
-
Koonin, E.V.1
Wolf, Y.I.2
Kondrashov, A.S.3
Aravind, L.4
-
22
-
-
0034889360
-
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system
-
Aravind,L. and Koonin,E.V. (2001) Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res., 11, 1365-1374.
-
(2001)
Genome Res.
, vol.11
, pp. 1365-1374
-
-
Aravind, L.1
Koonin, E.V.2
-
23
-
-
7444269607
-
Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine
-
Della,M., Palmbos,P.L., Tseng,H.-M., Tonkin,L.M., Daley,J.M., Topper,L.M., Pitcher,R.S., Tomkinson,A.E., Wilson,T.E. and Doherty,A.J. (2004) Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science, 306, 683-685.
-
(2004)
Science
, vol.306
, pp. 683-685
-
-
Della, M.1
Palmbos, P.L.2
Tseng, H.-M.3
Tonkin, L.M.4
Daley, J.M.5
Topper, L.M.6
Pitcher, R.S.7
Tomkinson, A.E.8
Wilson, T.E.9
Doherty, A.J.10
-
24
-
-
2342466121
-
The replication protein of the Sulfolobus islandicus plasmid pRN1
-
Lipps,G. (2004) The replication protein of the Sulfolobus islandicus plasmid pRN1. Biochem. Soc. Trans., 32, 240-244.
-
(2004)
Biochem. Soc. Trans.
, vol.32
, pp. 240-244
-
-
Lipps, G.1
-
25
-
-
0742305294
-
Structure of a bifunctional DNA primase-polymerase
-
Lipps,G., Weinzierl,A.O., von Scheven,G., Buchen,C. and Cramer,P. (2004) Structure of a bifunctional DNA primase-polymerase. Nat. Struct. Mol. Biol., 11, 157-162.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 157-162
-
-
Lipps, G.1
Weinzierl, A.O.2
von Scheven, G.3
Buchen, C.4
Cramer, P.5
-
26
-
-
0028278095
-
Helicase-primase complex of herpes simplex virus type 1: A mutation in the UL52 subunit abolishes primase activity
-
Klinedinst,D.K. and Challberg,M.D. (1994) Helicase-primase complex of herpes simplex virus type 1: A mutation in the UL52 subunit abolishes primase activity. J. Virol., 68, 3693-3701.
-
(1994)
J. Virol.
, vol.68
, pp. 3693-3701
-
-
Klinedinst, D.K.1
Challberg, M.D.2
-
27
-
-
0028998313
-
Identification of the primase active site of the herpes simplex virus type 1 helicase-primase
-
Dracheva,S., Koonin,E.V. and Crute,J.J. (1995) Identification of the primase active site of the herpes simplex virus type 1 helicase-primase. J. Biol. Chem., 270, 14148-14153.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 14148-14153
-
-
Dracheva, S.1
Koonin, E.V.2
Crute, J.J.3
-
28
-
-
0028834276
-
Primer RNA synthesis by plasmid-specified Rep protein for initiation of Co1E2 DNA replication
-
Takechi,S., Matsui,H. and Itoh,T. (1995) Primer RNA synthesis by plasmid-specified Rep protein for initiation of Co1E2 DNA replication. EMBO J., 14, 5141-5147.
-
(1995)
EMBO J.
, vol.14
, pp. 5141-5147
-
-
Takechi, S.1
Matsui, H.2
Itoh, T.3
-
29
-
-
0028881861
-
Initiation of unidirectional Co1E2 DNA replication by a unique priming mechanism
-
Takechi,S. and Itoh,T. (1995) Initiation of unidirectional Co1E2 DNA replication by a unique priming mechanism. Nucleic Acids Res., 23, 4196-4201.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 4196-4201
-
-
Takechi, S.1
Itoh, T.2
-
30
-
-
0030801002
-
Gapped BLAST and PST-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PST-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
31
-
-
0031743421
-
Profile hidden Markov models
-
Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
32
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
33
-
-
0029144601
-
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
-
Neuwald,A.F., Liu,J.S. and Lawrence,C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci. 4, 1618-1632.
-
(1995)
Protein Sci.
, vol.4
, pp. 1618-1632
-
-
Neuwald, A.F.1
Liu, J.S.2
Lawrence, C.E.3
-
34
-
-
0026100921
-
A workbench for multiple alignment construction and analysis
-
Schuler,G.D., Altschul,S.F. and Lipman,D.J. (1991) A workbench for multiple alignment construction and analysis. Proteins, 9, 180-190.
-
(1991)
Proteins
, vol.9
, pp. 180-190
-
-
Schuler, G.D.1
Altschul, S.F.2
Lipman, D.J.3
-
35
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
36
-
-
0034623005
-
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
-
37
-
-
0037433034
-
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
-
-
0032420333
-
JPred: A consensus secondary structure prediction server
-
Cuff,J.A., Clamp,M.E., Siddiqui,A.S., Finlay,M. and Barton,G.J. (1999) JPred: A consensus secondary structure prediction server. Bioinformatics, 14, 892-893.
-
(1999)
Bioinformatics
, vol.14
, pp. 892-893
-
-
Cuff, J.A.1
Clamp, M.E.2
Siddiqui, A.S.3
Finlay, M.4
Barton, G.J.5
-
40
-
-
0034663597
-
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
-
Cuff,J.A. and Barton,G.J. (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
-
(2000)
Proteins
, vol.40
, pp. 502-511
-
-
Cuff, J.A.1
Barton, G.J.2
-
41
-
-
0026244229
-
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. Crystallogr., 24, 946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
42
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
43
-
-
0029918694
-
The FSSP database: Fold classification based on structure-structure alignment of proteins
-
Holm,L. and Sander,C. (1996) The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucleic Acids Res., 24, 206-209.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 206-209
-
-
Holm, L.1
Sander, C.2
-
44
-
-
0028871926
-
Dali: A network tool for protein structure comparison
-
Holm,L. and Sander,C. (1995) Dali: A network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 478-480
-
-
Holm, L.1
Sander, C.2
-
45
-
-
0029936121
-
Surprising similarities in structure comparison
-
Gibrat,J.F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 377-385
-
-
Gibrat, J.F.1
Madej, T.2
Bryant, S.H.3
-
46
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein,J. (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol., 266, 418-427.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
47
-
-
0025873443
-
On the maximum likelihood method in molecular phylogenetics
-
Hasegawa,M., Kishino,H. and Saitou,N. (1991) On the maximum likelihood method in molecular phylogenetics. J. Mol. Evol., 32, 443-445.
-
(1991)
J. Mol. Evol.
, vol.32
, pp. 443-445
-
-
Hasegawa, M.1
Kishino, H.2
Saitou, N.3
-
48
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf,Y.I., Rogozin,I.B., Grishin,N.V., Tatusov,R.L. and Koonin,E.V. (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol., 1, 8.
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
49
-
-
9244224132
-
The heterodimeric primase of the hyperthermophilic archaeon Sulfolobus solfataricus possesses DNA and RNA primase, polymerase and 3′-terminal nucleotidyl transferase activities
-
Lao-Sirieix,S.-h. and Bell,S.D. (2004) The heterodimeric primase of the hyperthermophilic archaeon Sulfolobus solfataricus possesses DNA and RNA primase, polymerase and 3′-terminal nucleotidyl transferase activities. J. Mol. Biol., 344, 1251-1263.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1251-1263
-
-
Lao-Sirieix, S.-H.1
Bell, S.D.2
-
50
-
-
0033564245
-
Arg304 of human DNA primase is a key contributor to catalysis and NTP binding: Primase and the family X polymerases share significant sequence homology
-
Kirk,B.W. and Kuchta,R.D. (1999) Arg304 of human DNA primase is a key contributor to catalysis and NTP binding: Primase and the family X polymerases share significant sequence homology. Biochemistry, 38, 7727-7736.
-
(1999)
Biochemistry
, vol.38
, pp. 7727-7736
-
-
Kirk, B.W.1
Kuchta, R.D.2
-
51
-
-
0033119535
-
DNA polymerase beta-like nucleotidyltransferase superfamily: Identification of three new families, classification and evolutionary history
-
Aravind,L. and Koonin,E.V. (1999) DNA polymerase beta-like nucleotidyltransferase superfamily: Identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27, 1609-1618.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 1609-1618
-
-
Aravind, L.1
Koonin, E.V.2
-
52
-
-
0032518374
-
A mechanism for all polymerases
-
Steitz,T.A. (1998) A mechanism for all polymerases. Nature, 391 231-232.
-
(1998)
Nature
, vol.391
, pp. 231-232
-
-
Steitz, T.A.1
-
53
-
-
0036678683
-
The structure of a replication initiator unites diverse aspects of nucleic acid metabolism
-
Campos-Olivas,R., Louis,J.M., Clerot,D., Gronenborn,B. and Gronenborn,A.M. (2002) The structure of a replication initiator unites diverse aspects of nucleic acid metabolism. Proc. Natl Acad. Sci. USA 99, 10310-10315.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 10310-10315
-
-
Campos-Olivas, R.1
Louis, J.M.2
Clerot, D.3
Gronenborn, B.4
Gronenborn, A.M.5
-
54
-
-
0033634815
-
Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus
-
Enemark,E.J., Chen,G., Vaughn,D.E., Stenlund,A. and Joshua-Tor,L. (2000) Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Mol. Cell., 6, 149-158.
-
(2000)
Mol. Cell.
, vol.6
, pp. 149-158
-
-
Enemark, E.J.1
Chen, G.2
Vaughn, D.E.3
Stenlund, A.4
Joshua-Tor, L.5
-
55
-
-
0030443808
-
Solution structure of the origin DNA-binding domain of SV40 T-antigen
-
Luo,X., Sanford,D.G., Bullock,P.A. and Bachovchin,W.W. (1996) Solution structure of the origin DNA-binding domain of SV40 T-antigen. Nature Struct. Biol., 3, 1034-1039.
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 1034-1039
-
-
Luo, X.1
Sanford, D.G.2
Bullock, P.A.3
Bachovchin, W.W.4
-
56
-
-
0036671409
-
Structural unity among viral origin binding proteins: Crystal structure of the nuclease domain of adeno-associated virus Rep
-
Hickman,A.B., Ronning,D.R., Kotin,R.M. and Dyda,F. (2002) Structural unity among viral origin binding proteins: Crystal structure of the nuclease domain of adeno-associated virus Rep. Mol. Cell., 10 327-337.
-
(2002)
Mol. Cell.
, vol.10
, pp. 327-337
-
-
Hickman, A.B.1
Ronning, D.R.2
Kotin, R.M.3
Dyda, F.4
-
57
-
-
0242542025
-
Structural insights into single-stranded DNA binding and cleavage by F factor TraI
-
Datta,S., Larkin,C. and Schildbach,J.F. (2003) Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure (Camb), 11, 1369-1379.
-
(2003)
Structure (Camb.)
, vol.11
, pp. 1369-1379
-
-
Datta, S.1
Larkin, C.2
Schildbach, J.F.3
-
58
-
-
2642580884
-
T antigen origin-binding domain of simian virus 40: Determinants of specific DNA binding
-
Bradshaw,E.M., Sanford,D.G., Luo,X., Sudmeier,J.L., Gurard-Levin,Z.A., Bullock,P.A. and Bachovchin,W.W. (2004) T antigen origin-binding domain of simian virus 40: Determinants of specific DNA binding. Biochemistry, 43, 6928-6936.
-
(2004)
Biochemistry
, vol.43
, pp. 6928-6936
-
-
Bradshaw, E.M.1
Sanford, D.G.2
Luo, X.3
Sudmeier, J.L.4
Gurard-Levin, Z.A.5
Bullock, P.A.6
Bachovchin, W.W.7
-
59
-
-
1242339574
-
The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces
-
Hickman,A.B., Ronning,D.R., Perez,Z.N., Kotin,R.M. and Dyda,F. (2004) The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces. Mol. Cell., 13, 403-414.
-
(2004)
Mol. Cell.
, vol.13
, pp. 403-414
-
-
Hickman, A.B.1
Ronning, D.R.2
Perez, Z.N.3
Kotin, R.M.4
Dyda, F.5
-
60
-
-
12944319325
-
Eukaryotic/archaeal primase and MCM proteins encoded in a bacteriophage genome
-
McGeoch,A.T. and Bell,S.D. (2005) Eukaryotic/archaeal primase and MCM proteins encoded in a bacteriophage genome. Cell, 120, 167-168.
-
(2005)
Cell
, vol.120
, pp. 167-168
-
-
McGeoch, A.T.1
Bell, S.D.2
-
61
-
-
0345733993
-
Distinct domain functions regulating de novo DNA synthesis of thermostable DNA primase from hyperthermophile Pyrococcus horikoshii
-
Matsui,E., Nishio,M., Yokoyama,H., Harata,K., Darnis,S. and Matsui,I. (2003) Distinct domain functions regulating de novo DNA synthesis of thermostable DNA primase from hyperthermophile Pyrococcus horikoshii. Biochemistry, 42, 14968-14976.
-
(2003)
Biochemistry
, vol.42
, pp. 14968-14976
-
-
Matsui, E.1
Nishio, M.2
Yokoyama, H.3
Harata, K.4
Darnis, S.5
Matsui, I.6
-
62
-
-
0038682956
-
Replication of the baculovirus genome
-
Mikhailov,V.S. (2003) Replication of the baculovirus genome. Mol. Biol. (Mosk), 37, 288-299.
-
(2003)
Mol. Biol. (Mosk.)
, vol.37
, pp. 288-299
-
-
Mikhailov, V.S.1
-
63
-
-
0024362546
-
A single essential gene, PRI2, encodes the large subunit of DNA primase in Saccharomyces cerevisiae
-
Foiani,M., Santocanale,C., Plevani,P. and Lucchini,G. (1989) A single essential gene, PRI2, encodes the large subunit of DNA primase in Saccharomyces cerevisiae. Mol. Cell. Biol., 9, 3081-3087.
-
(1989)
Mol. Cell. Biol.
, vol.9
, pp. 3081-3087
-
-
Foiani, M.1
Santocanale, C.2
Plevani, P.3
Lucchini, G.4
-
64
-
-
0030947916
-
Characterization of the interaction between the baculovirus replication factors LEF-1 and LEF-2
-
Evans,J.T., Leisy,D.J. and Rohrmann,G.F. (1997) Characterization of the interaction between the baculovirus replication factors LEF-1 and LEF-2. J. Virol., 71, 3114-3119.
-
(1997)
J. Virol.
, vol.71
, pp. 3114-3119
-
-
Evans, J.T.1
Leisy, D.J.2
Rohrmann, G.F.3
-
65
-
-
9144244444
-
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52
-
Iyer,L.M., Koonin,E.V. and Aravind,L. (2002) Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics, 3, 8.
-
(2002)
BMC Genomics
, vol.3
, pp. 8
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
66
-
-
5144223072
-
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: Implications for the origins of chromosome segregation, cell division and viral capsid packaging
-
Iyer,L.M., Makarova,K.S., Koonin,E.V. and Aravind,L. (2004) Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: Implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res., 32, 5260-5279.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5260-5279
-
-
Iyer, L.M.1
Makarova, K.S.2
Koonin, E.V.3
Aravind, L.4
-
68
-
-
0029863918
-
Specificity determinants in interaction of the initiator (Rep) proteins with the origins in the plasmids Co1E2-P9 and Co1E3-CA38 identified by chimera analysis
-
Shinohara,M. and Itoh,T. (1996) Specificity determinants in interaction of the initiator (Rep) proteins with the origins in the plasmids Co1E2-P9 and Co1E3-CA38 identified by chimera analysis. J. Mol. Biol. 257, 290-300.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 290-300
-
-
Shinohara, M.1
Itoh, T.2
-
69
-
-
17944395486
-
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors
-
Iyer,L.M., Koonin,E.V. and Aravind,L. (2002) Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Genome Biol., 3
-
(2002)
Genome Biol.
, vol.3
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
70
-
-
1642325936
-
Evolutionary history and higher order classification of AAA+ ATPases
-
Iyer,L.M., Leipe,D.D., Koonin,E.V. and Aravind,L. (2004) Evolutionary history and higher order classification of AAA+ ATPases. J. Struct. Biol., 146, 11-31.
-
(2004)
J. Struct. Biol.
, vol.146
, pp. 11-31
-
-
Iyer, L.M.1
Leipe, D.D.2
Koonin, E.V.3
Aravind, L.4
-
71
-
-
0035167322
-
Common origin of four diverse families of large eukaryotic DNA viruses
-
Iyer,L.M., Aravind,L. and Koonin,E.V. (2001) Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol., 75 11720-11734.
-
(2001)
J. Virol.
, vol.75
, pp. 11720-11734
-
-
Iyer, L.M.1
Aravind, L.2
Koonin, E.V.3
-
72
-
-
0032881250
-
MCM proteins in DNA replication
-
Tye,B.K. (1999) MCM proteins in DNA replication. Annu. Rev. Biochem. 68, 649-686.
-
(1999)
Annu. Rev. Biochem.
, vol.68
, pp. 649-686
-
-
Tye, B.K.1
-
73
-
-
0033975419
-
The bacterial replicative helicase DnaB evolved from a RecA duplication
-
Leipe,D.D., Aravind,L., Grishin,N.V. and Koonin,E.V. (2000) The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res., 10, 5-16.
-
(2000)
Genome Res.
, vol.10
, pp. 5-16
-
-
Leipe, D.D.1
Aravind, L.2
Grishin, N.V.3
Koonin, E.V.4
-
74
-
-
0029856618
-
Crystal structure of a DExx box DNA helicase
-
Subramanya,H.S., Bird,L.E., Brannigan,J.A. and Wigley,D.B. (1996) Crystal structure of a DExx box DNA helicase. Nature, 384, 379-383.
-
(1996)
Nature
, vol.384
, pp. 379-383
-
-
Subramanya, H.S.1
Bird, L.E.2
Brannigan, J.A.3
Wigley, D.B.4
-
75
-
-
0035121915
-
Bacterial conjugation: Running rings around DNA
-
Egelman,E.H. (2001) Bacterial conjugation: Running rings around DNA. Curr. Biol., 11, 103-105.
-
(2001)
Curr. Biol.
, vol.11
, pp. 103-105
-
-
Egelman, E.H.1
-
76
-
-
0033583318
-
2+ finger motif of UL52 severely affects the biochemical activities of the HSV-1 helicase-primase subcomplex
-
2+ finger motif of UL52 severely affects the biochemical activities of the HSV-1 helicase-primase subcomplex. Curr. Biol., 274, 8068-8076.
-
(1999)
Curr. Biol.
, vol.274
, pp. 8068-8076
-
-
Biswas, N.1
Weller, S.K.2
-
77
-
-
0034653865
-
Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase
-
Pan,H. and Wigley,D.B. (2000) Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Structure Fold Des., 8, 231-239.
-
(2000)
Structure Fold Des.
, vol.8
, pp. 231-239
-
-
Pan, H.1
Wigley, D.B.2
-
78
-
-
0033551040
-
The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition
-
Kusakabe,T., Hine,A.V., Hyberts,S.G. and Richardson,C.C. (1999) The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition. Proc. Natl Acad. Sci. USA, 96 4295-4300.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4295-4300
-
-
Kusakabe, T.1
Hine, A.V.2
Hyberts, S.G.3
Richardson, C.C.4
-
79
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
80
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
Wolf,Y.I., Rogozin,I.B., Kondrashov,A.S. and Koonin,E.V. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res., 11, 356-372.
-
(2001)
Genome Res.
, vol.11
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
81
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen,M., Snel,B., Lathe,W.,III and Bork,P. (2000) Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe III, W.3
Bork, P.4
-
82
-
-
0035196036
-
Spatial regulation of cytokinesis in bacteria
-
Margolin,W. (2001) Spatial regulation of cytokinesis in bacteria. Curr. Opin. Microbiol., 4, 647-652.
-
(2001)
Curr. Opin. Microbiol.
, vol.4
, pp. 647-652
-
-
Margolin, W.1
-
83
-
-
0035907374
-
Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases
-
Handa,P., Acharya,N. and Varshney,U. (2001) Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases. J. Biol. Chem., 276, 16992-16997.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 16992-16997
-
-
Handa, P.1
Acharya, N.2
Varshney, U.3
-
84
-
-
0034074478
-
Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease
-
Genschel,J., Curth,U. and Urbanke,C. (2000) Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease. J. Biol. Chem., 381, 183-192.
-
(2000)
J. Biol. Chem.
, vol.381
, pp. 183-192
-
-
Genschel, J.1
Curth, U.2
Urbanke, C.3
-
85
-
-
0032522760
-
Devoted to the tagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly
-
Kelman,Z., Yuzhakov,A., Andjelkovic,J. and O'Donnell,M. (1998) Devoted to the tagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J., 17, 2436-2449.
-
(1998)
EMBO J.
, vol.17
, pp. 2436-2449
-
-
Kelman, Z.1
Yuzhakov, A.2
Andjelkovic, J.3
O'Donnell, M.4
-
86
-
-
13444282478
-
PriA helicase and SSB interact physically and functionally
-
Cadman,C.J. and McGlynn,P. (2004) PriA helicase and SSB interact physically and functionally. Nucleic Acids Res., 32, 6378-6387.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 6378-6387
-
-
Cadman, C.J.1
McGlynn, P.2
-
87
-
-
0037108889
-
Structure of the single-strand annealing domain of human RAD52 protein
-
Singleton,M.R., Wentzell,L.M., Liu,Y., West,S.C. and Wigley,D.B. (2002) Structure of the single-strand annealing domain of human RAD52 protein. Proc. Natl Acad. Sci. USA, 99, 13492-13497.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13492-13497
-
-
Singleton, M.R.1
Wentzell, L.M.2
Liu, Y.3
West, S.C.4
Wigley, D.B.5
-
88
-
-
0026704305
-
Organization and evolution of bacterial and bacteriophage primase-helicase systems
-
Ilyina,T.V., Gorbalenya,A.E. and Koonin,E.V. (1992) Organization and evolution of bacterial and bacteriophage primase-helicase systems. J. Mol. Evol., 34, 351-357.
-
(1992)
J. Mol. Evol.
, vol.34
, pp. 351-357
-
-
Ilyina, T.V.1
Gorbalenya, A.E.2
Koonin, E.V.3
-
89
-
-
0021891888
-
DNA topoisomerases
-
Wang,J.C. (1985) DNA topoisomerases. Annu. Rev. Biochem., 54 665-697.
-
(1985)
Annu. Rev. Biochem.
, vol.54
, pp. 665-697
-
-
Wang, J.C.1
-
90
-
-
0024291345
-
A novel reverse transcriptase activity associated with mitochondrial plasmids of Neurospora
-
Kuiper,M.T. and Lambowitz,A.M. (1988) A novel reverse transcriptase activity associated with mitochondrial plasmids of Neurospora. Cell 55, 693-704.
-
(1988)
Cell
, vol.55
, pp. 693-704
-
-
Kuiper, M.T.1
Lambowitz, A.M.2
-
91
-
-
0036790008
-
The origin of DNA genomes and DNA replication proteins
-
Forterre,P. (2002) The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol., 5, 525-532.
-
(2002)
Curr. Opin. Microbiol.
, vol.5
, pp. 525-532
-
-
Forterre, P.1
-
92
-
-
0033571463
-
Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus
-
Ago,H., Adachi,T., Yoshida,A., Yamamoto,M., Habuka,N., Yatsunami,K. and Miyano,M. (1999) Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Struct. Fold. Des., 7, 1417-1426.
-
(1999)
Struct. Fold. Des.
, vol.7
, pp. 1417-1426
-
-
Ago, H.1
Adachi, T.2
Yoshida, A.3
Yamamoto, M.4
Habuka, N.5
Yatsunami, K.6
Miyano, M.7
-
93
-
-
0029645414
-
Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase
-
Georgiadis,M.M., Jessen,S.M., Ogata,C.M., Telesnitsky,A., Goff,S.P. and Hendrickson,W.A. (1995) Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase. Structure, 3, 879-892.
-
(1995)
Structure
, vol.3
, pp. 879-892
-
-
Georgiadis, M.M.1
Jessen, S.M.2
Ogata, C.M.3
Telesnitsky, A.4
Goff, S.P.5
Hendrickson, W.A.6
-
94
-
-
0033616725
-
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius
-
Hopfner,K.P., Eichinger,A., Engh,R.A., Laue,F., Ankenbauer,W., Huber,R. and Angerer,B. (1999) Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc. Natl Acad. Sci. USA 96, 3600-3605.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 3600-3605
-
-
Hopfner, K.P.1
Eichinger, A.2
Engh, R.A.3
Laue, F.4
Ankenbauer, W.5
Huber, R.6
Angerer, B.7
-
95
-
-
0028983795
-
Crystal structure of Thermus aquaticus DNA polymerase
-
Kim.Y., Eom,S.H., Wang,J., Lee,D.S., Suh,S.W. and Steitz,T.A. (1995) Crystal structure of Thermus aquaticus DNA polymerase. Nature 376, 612-616.
-
(1995)
Nature
, vol.376
, pp. 612-616
-
-
Kim, Y.1
Eom, S.H.2
Wang, J.3
Lee, D.S.4
Suh, S.W.5
Steitz, T.A.6
-
96
-
-
0035254334
-
Structural analysis of adenylate cyclases from Trypanosoma brucei in their monomeric state
-
Bieger,B. and Essen,L.O. (2001) Structural analysis of adenylate cyclases from Trypanosoma brucei in their monomeric state. EMBO J., 20, 433-445.
-
(2001)
EMBO J.
, vol.20
, pp. 433-445
-
-
Bieger, B.1
Essen, L.O.2
|