Nucleic Acids Research, Vol 26, Issue 2 391-406, Copyright © 1998 by Oxford University Press
SE Nunes-Duby, HJ Kwon, RS Tirumalai, T Ellenberger and A Landy
Alignments of 105 site-specific recombinases belonging to the Int family of
proteins identified extended areas of similarity and three types of
structural differences. In addition to the previously recognized
conservation of the tetrad R-H-R-Y, located in boxes I and II, several
newly identified sequence patches include charged amino acids that are
highly conserved and a specific pattern of buried residues contributing to
the overall protein fold. With some notable exceptions, unconserved regions
correspond to loops in the crystal structures of the catalytic domains of
lambda Int (Int c170) and HP1 Int (HPC) and of the recombinases XerD and
Cre. Two structured regions also harbor some pronounced differences. The
first comprises beta- sheets 4 and 5, alpha-helix D and the adjacent loop
connecting it to alpha-helix E: two Ints of phages infecting thermophilic
bacteria are missing this region altogether; the crystal structures of HPC,
XerD and Cre reveal a lack of beta-sheets 4 and 5; Cre displays two
additional beta-sheets following alpha-helix D; five recombinases carry
large insertions. The second involves the catalytic tyrosine and is seen in
a comparison of the four crystal structures. The yeast recombinases can
theoretically be fitted to the Int fold, but the overall differences,
involving changes in spacing as well as in motif structure, are more
substantial than seen in most other proteins. The phenotypes of mutations
compiled from several proteins are correlated with the available structural
information and structure-function relationships are discussed. In
addition, a few prokaryotic and eukaryotic enzymes with partial homology
with the Int family of recombinases may be distantly related, either
through divergent or convergent evolution. These include a restriction
enzyme and a subgroup of eukaryotic RNA helicases (D-E-A-D proteins).
ARTICLES
Similarities and differences among 105 members of the Int family of site-specific recombinases
Division of Biology and Medicine, Brown University, Providence, RI 02912, USA. simone_nunes-duby@brown.edu
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E. Gindreau, R. López, and P. García MM1, a Temperate Bacteriophage of the Type 23F Spanish/USA Multiresistant Epidemic Clone of Streptococcus pneumoniae: Structural Analysis of the Site-Specific Integration System J. Virol., September 1, 2000; 74(17): 7803 - 7813. [Abstract] [Full Text]
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Q. Cheng, B. J. Paszkiet, N. B. Shoemaker, J. F. Gardner, and A. A. Salyers Integration and Excision of a Bacteroides Conjugative Transposon, CTnDOT J. Bacteriol., July 15, 2000; 182(14): 4035 - 4043. [Abstract] [Full Text]
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C. E. A. Peña, J. M. Kahlenberg, and G. F. Hatfull Assembly and activation of site-specific recombination complexes PNAS, June 23, 2000; (2000) 140014297. [Abstract] [Full Text]
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J. Wang, N. B. Shoemaker, G.-R. Wang, and A. A. Salyers Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene J. Bacteriol., June 15, 2000; 182(12): 3559 - 3571. [Abstract] [Full Text]
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N. V. Grishin Two tricks in one bundle: helix-turn-helix gains enzymatic activity Nucleic Acids Res., June 1, 2000; 28(11): 2229 - 2233. [Abstract] [Full Text] [PDF]
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A. Gyohda and T. Komano Purification and Characterization of the R64 Shufflon-Specific Recombinase J. Bacteriol., May 15, 2000; 182(10): 2787 - 2792. [Abstract] [Full Text]
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L. S. Burns, S. G. J. Smith, and C. J. Dorman Interaction of the FimB Integrase with the fimS Invertible DNA Element in Escherichia coli In Vivo and In Vitro J. Bacteriol., May 15, 2000; 182(10): 2953 - 2959. [Abstract] [Full Text]
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G. J. Poelarends, L. A. Kulakov, M. J. Larkin, J. E. T. van Hylckama Vlieg, and D. B. Janssen Roles of Horizontal Gene Transfer and Gene Integration in Evolution of 1,3-Dichloropropene- and 1,2-Dibromoethane-Degradative Pathways J. Bacteriol., April 15, 2000; 182(8): 2191 - 2199. [Abstract] [Full Text]
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L. Jessop, T. Bankhead, D. Wong, and A. M. Segall The Amino Terminus of Bacteriophage lambda Integrase Is Involved in Protein-Protein Interactions during Recombination J. Bacteriol., February 15, 2000; 182(4): 1024 - 1034. [Abstract] [Full Text]
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F. Auvray, M. Coddeville, R. C. Ordonez, and P. Ritzenthaler Unusual Structure of the attB Site of the Site-Specific Recombination System of Lactobacillus delbrueckii Bacteriophage mv4 J. Bacteriol., December 1, 1999; 181(23): 7385 - 7389. [Abstract] [Full Text]
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T. Liu and E. Haggård-Ljungquist The Transcriptional Switch of Bacteriophage WPhi , a P2-Related but Heteroimmune Coliphage J. Virol., December 1, 1999; 73(12): 9816 - 9826. [Abstract] [Full Text]
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A. Petersen, J. Josephsen, and M. G. Johnsen TPW22, a Lactococcal Temperate Phage with a Site-Specific Integrase Closely Related to Streptococcus thermophilus Phage Integrases J. Bacteriol., November 15, 1999; 181(22): 7034 - 7042. [Abstract] [Full Text]
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S. Semsey, I. Papp, Z. Buzas, A. Patthy, L. Orosz, and P. P. Papp Identification of Site-Specific Recombination Genes int and xis of the Rhizobium Temperate Phage 16-3 J. Bacteriol., July 15, 1999; 181(14): 4185 - 4192. [Abstract] [Full Text]
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E. H. Cho, C.-E. Nam, R. Alcaraz Jr., and J. F. Gardner Site-Specific Recombination of Bacteriophage P22 Does Not Require Integration Host Factor J. Bacteriol., July 15, 1999; 181(14): 4245 - 4249. [Abstract] [Full Text]
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F. Guo, D. N. Gopaul, and G. D. Van Duyne Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse PNAS, June 22, 1999; 96(13): 7143 - 7148. [Abstract] [Full Text] [PDF]
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S. Yang and L. K. Miller Activation of Baculovirus Very Late Promoters by Interaction with Very Late Factor 1 J. Virol., April 1, 1999; 73(4): 3404 - 3409. [Abstract] [Full Text]
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I. Grainge and D. J. Sherratt Xer Site-specific Recombination. DNA STRAND REJOINING BY RECOMBINASE XerC J. Biol. Chem., March 5, 1999; 274(10): 6763 - 6769. [Abstract] [Full Text] [PDF]
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C. E. A. Peña, J. M. Kahlenberg, and G. F. Hatfull Protein-DNA Complexes in Mycobacteriophage L5 Integrative Recombination J. Bacteriol., January 15, 1999; 181(2): 454 - 461. [Abstract] [Full Text]
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L. L. Voelker and K. Dybvig Characterization of the Lysogenic Bacteriophage MAV1 from Mycoplasma arthritidis J. Bacteriol., November 15, 1998; 180(22): 5928 - 5931. [Abstract] [Full Text]
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C.-J. Xu, Y.-T. Ahn, S. Pathania, and M. Jayaram Flp Ribonuclease Activities. MECHANISTIC SIMILARITIES AND CONTRASTS TO SITE-SPECIFIC DNA RECOMBINATION J. Biol. Chem., November 13, 1998; 273(46): 30591 - 30598. [Abstract] [Full Text] [PDF]
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