Nucleic Acids Research, Vol 25, Issue 18 3605-3614, Copyright © 1997 by Oxford University Press
D Esposito and JJ Scocca
The integrases are a diverse family of tyrosine recombinases which
rearrange DNA duplexes by means of conservative site-specific recombination
reactions. Members of this family, of which the well- studied lambda Int
protein is the prototype, were previously found to share four strongly
conserved residues, including an active site tyrosine directly involved in
transesterification. However, few additional sequence similarities were
found in the original group of 27 proteins. We have now identified a total
of 81 members of the integrase family deposited in the databases. Alignment
and comparisons of these sequences combined with an evolutionary analysis
aided in identifying broader sequence similarities and clarifying the
possible functions of these conserved residues. This analysis showed that
members of the family aggregate into subfamilies which are consistent with
their biological roles; these subfamilies have significant levels of
sequence similarity beyond the four residues previously identified. It was
also possible to map the location of conserved residues onto the available
crystal structures; most of the conserved residues cluster in the predicted
active site cleft. In addition, these results offer clues into an apparent
discrepancy between the mechanisms of different subfamilies of integrases.
ARTICLES
The integrase family of tyrosine recombinases: evolution of a conserved active site domain
Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 5 Center Drive MSC0560, Bethesda, MD 20782, USA. domespo@helix.nih.gov
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. C. M. Fogg, S. M. Gossage, D. L. Smith, J. R. Saunders, A. J. McCarthy, and H. E. Allison Identification of multiple integration sites for Stx-phage {Phi}24B in the Escherichia coli genome, description of a novel integrase and evidence for a functional anti-repressor Microbiology, December 1, 2007; 153(12): 4098 - 4110. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Flanigan and J. F. Gardner Interaction of the Gifsy-1 Xis Protein with the Gifsy-1 attP Sequence J. Bacteriol., September 1, 2007; 189(17): 6303 - 6311. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Qiu, A. U. Gurkar, and S. Lory Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa PNAS, December 26, 2006; 103(52): 19830 - 19835. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Piazzolla, S. Cali, E. Spoldi, F. Forti, C. Sala, F. Magnoni, G. Deho, and D. Ghisotti Expression of phage P4 integrase is regulated negatively by both Int and Vis. J. Gen. Virol., August 1, 2006; 87(Pt 8): 2423 - 2431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Erauso, K. M. Stedman, H. J. G. van de Werken, W. Zillig, and J. van der Oost Two novel conjugative plasmids from a single strain of Sulfolobus Microbiology, July 1, 2006; 152(7): 1951 - 1968. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bryan, P. Roesch, L. Davis, R. Moritz, S. Pellett, and R. A. Welch Regulation of Type 1 Fimbriae by Unlinked FimB- and FimE-Like Recombinases in Uropathogenic Escherichia coli Strain CFT073 Infect. Immun., February 1, 2006; 74(2): 1072 - 1083. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. H. Paul, S. J. Williamson, A. Long, R. N. Authement, D. John, A. M. Segall, F. L. Rohwer, M. Androlewicz, and S. Patterson Complete Genome Sequence of {phi}HSIC, a Pseudotemperate Marine Phage of Listonella pelagia Appl. Envir. Microbiol., June 1, 2005; 71(6): 3311 - 3320. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Ghosh, C. K. Lau, F. Guo, A. M. Segall, and G. D. Van Duyne Peptide Trapping of the Holliday Junction Intermediate in Cre-loxP Site-specific Recombination J. Biol. Chem., March 4, 2005; 280(9): 8290 - 8299. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T.-A. Mistretta and L. A. Guarino Transcriptional Activity of Baculovirus Very Late Factor 1 J. Virol., February 1, 2005; 79(3): 1958 - 1960. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Deneke, A. B. Burgin, S. L. Wilson, and G. Chaconas Catalytic Residues of the Telomere Resolvase ResT: A PATTERN SIMILAR TO, BUT DISTINCT FROM, TYROSINE RECOMBINASES AND TYPE IB TOPOISOMERASES J. Biol. Chem., December 17, 2004; 279(51): 53699 - 53706. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Brom, L. Girard, C. Tun-Garrido, A. Garcia-de los Santos, P. Bustos, V. Gonzalez, and D. Romero Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42 Requires Cointegration with p42a, Which May Be Mediated by Site-Specific Recombination J. Bacteriol., November 15, 2004; 186(22): 7538 - 7548. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Johansson, M. Kamali-Moghaddam, and L. Sundstrom Integron integrase binds to bulged hairpin DNA Nucleic Acids Res., August 2, 2004; 32(13): 4033 - 4043. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Letzelter, M. Duguet, and M.-C. Serre Mutational Analysis of the Archaeal Tyrosine Recombinase SSV1 Integrase Suggests a Mechanism of DNA Cleavage in trans J. Biol. Chem., July 9, 2004; 279(28): 28936 - 28944. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Bueno, C. A. Santiviago, A. A. Murillo, J. A. Fuentes, A. N. Trombert, P. I. Rodas, P. Youderian, and G. C. Mora Precise Excision of the Large Pathogenicity Island, SPI7, in Salmonella enterica Serovar Typhi J. Bacteriol., May 15, 2004; 186(10): 3202 - 3213. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Nemergut, A. P. Martin, and S. K. Schmidt Integron Diversity in Heavy-Metal-Contaminated Mine Tailings and Inferences about Integron Evolution Appl. Envir. Microbiol., February 1, 2004; 70(2): 1160 - 1168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Boldt, C. Pinilla, and A. M. Segall Reversible Inhibitors of {lambda} Integrase-mediated Recombination Efficiently Trap Holliday Junction Intermediates and Form the Basis of a Novel Assay for Junction Resolution J. Biol. Chem., January 30, 2004; 279(5): 3472 - 3483. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Interthal, P. M. Quigley, W. G. J. Hol, and J. J. Champoux The Role of Lysine 532 in the Catalytic Mechanism of Human Topoisomerase I J. Biol. Chem., January 23, 2004; 279(4): 2984 - 2992. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. J. D. Goodwin, M. I. Butler, and R. T. M. Poulter Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi Microbiology, November 1, 2003; 149(11): 3099 - 3109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. C. Alexander, D. J. Devlin, D. D. Hewitt, A. C. Horan, and T. J. Hosted Development of the Micromonospora carbonacea var. africana ATCC 39149 bacteriophage pMLP1 integrase for site-specific integration in Micromonospora spp. Microbiology, September 1, 2003; 149(9): 2443 - 2453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. M. Swalla, R. I. Gumport, and J. F. Gardner Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain Nucleic Acids Res., February 1, 2003; 31(3): 805 - 818. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. E. Jacobs, A. Sanchez-Blanco, L. A. Katz, and L. A. Klobutcher Tec3, a New Developmentally Eliminated DNA Element in Euplotes crassus Eukaryot. Cell, February 1, 2003; 2(1): 103 - 114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Kazmierczak, B. M. Swalla, A. B. Burgin, R. I. Gumport, and J. F. Gardner Regulation of site-specific recombination by the C-terminus of {lambda} integrase Nucleic Acids Res., December 1, 2002; 30(23): 5193 - 5204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-T. T. Lesher, Y. Pommier, L. Stewart, and M. R. Redinbo 8-Oxoguanine rearranges the active site of human topoisomerase I PNAS, September 17, 2002; 99(19): 12102 - 12107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-C. Serre, C. Letzelter, J.-R. Garel, and M. Duguet Cleavage Properties of an Archaeal Site-specific Recombinase, the SSV1 Integrase J. Biol. Chem., May 3, 2002; 277(19): 16758 - 16767. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Kovach, R. Tirumalai, and A. Landy Site-specific Photo-cross-linking between lambda Integrase and Its DNA Recombination Target J. Biol. Chem., April 19, 2002; 277(17): 14530 - 14538. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Connolly, M. Iwahara, and R. T. Clubb Xis Protein Binding to the Left Arm Stimulates Excision of Conjugative Transposon Tn916 J. Bacteriol., April 15, 2002; 184(8): 2088 - 2099. [Abstract] [Full Text]
|
|
|
|
|
|
K. Hansson, L. Sundstrom, A. Pelletier, and P. H. Roy IntI2 Integron Integrase in Tn7 J. Bacteriol., March 15, 2002; 184(6): 1712 - 1721. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Drouin, J. Melancon, and P. H. Roy The IntI-Like Tyrosine Recombinase of Shewanella oneidensis Is Active as an Integron Integrase J. Bacteriol., March 15, 2002; 184(6): 1811 - 1815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Deneke, G. Ziegelin, R. Lurz, and E. Lanka Phage N15 Telomere Resolution. TARGET REQUIREMENTS FOR RECOGNITION AND PROCESSING BY THE PROTELOMERASE J. Biol. Chem., March 15, 2002; 277(12): 10410 - 10419. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. P. Williams Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies Nucleic Acids Res., February 15, 2002; 30(4): 866 - 875. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. I. Belova, R. Prasad, I. V. Nazimov, S. H. Wilson, and A. I. Slesarev The Domain Organization and Properties of Individual Domains of DNA Topoisomerase V, a Type 1B Topoisomerase with DNA Repair Activities J. Biol. Chem., February 8, 2002; 277(7): 4959 - 4965. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Sau, G. D. Tribble, I. Grainge, R. F. Frohlich, B. R. Knudsen, and M. Jayaram Biochemical and Kinetic Analysis of the RNase Active Sites of the Integrase/Tyrosine Family Site-specific DNA Recombinases J. Biol. Chem., November 30, 2001; 276(49): 46612 - 46623. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Messier and P. H. Roy Integron Integrases Possess a Unique Additional Domain Necessary for Activity J. Bacteriol., November 15, 2001; 183(22): 6699 - 6706. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. J. D. Goodwin and R. T. M. Poulter The DIRS1 Group of Retrotransposons Mol. Biol. Evol., November 1, 2001; 18(11): 2067 - 2082. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Esposito, J. S. Thrower, and J. J. Scocca Protein and DNA requirements of the bacteriophage HP1 recombination system: a model for intasome formation Nucleic Acids Res., October 1, 2001; 29(19): 3955 - 3964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Thyagarajan, E. C. Olivares, R. P. Hollis, D. S. Ginsburg, and M. P. Calos Site-Specific Genomic Integration in Mammalian Cells Mediated by Phage {phi}C31 Integrase Mol. Cell. Biol., June 15, 2001; 21(12): 3926 - 3934. [Abstract] [Full Text]
|
|
|
|
|
|
J. A. Lewis and G. F. Hatfull Control of directionality in integrase-mediated recombination: examination of recombination directionality factors (RDFs) including Xis and Cox proteins Nucleic Acids Res., June 1, 2001; 29(11): 2205 - 2216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Sciochetti, P. J. Piggot, and G. W. Blakely Identification and Characterization of the dif Site from Bacillus subtilis J. Bacteriol., February 1, 2001; 183(3): 1058 - 1068. [Abstract] [Full Text]
|
|
|
|
|
|
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]
|
|
|
|
|
|
J. Deneke, G. Ziegelin, R. Lurz, and E. Lanka The protelomerase of temperate Escherichia coli phage N15 has cleaving-joining activity PNAS, July 5, 2000; 97(14): 7721 - 7726. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
D. O'Sullivan, R. P. Ross, G. F. Fitzgerald, and A. Coffey Investigation of the Relationship between Lysogeny and Lysis of Lactococcus lactis in Cheese Using Prophage-Targeted PCR Appl. Envir. Microbiol., May 1, 2000; 66(5): 2192 - 2198. [Abstract] [Full Text]
|
|
|
|
|
|
G. W. Blakely, A. O. Davidson, and D. J. Sherratt Sequential Strand Exchange by XerC and XerD during Site-specific Recombination at dif J. Biol. Chem., March 31, 2000; 275(14): 9930 - 9936. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
B. Stentebjerg-Olesen, T. Chakraborty, and P. Klemm Type 1 Fimbriation and Phase Switching in a Natural Escherichia coli fimB Null Strain, Nissle 1917 J. Bacteriol., December 15, 1999; 181(24): 7470 - 7478. [Abstract] [Full Text]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
M. V. Francia, J. C. Zabala, F. de la Cruz, and J. M. García Lobo The IntI1 Integron Integrase Preferentially Binds Single-Stranded DNA of the attC Site J. Bacteriol., November 1, 1999; 181(21): 6844 - 6849. [Abstract] [Full Text]
|
|
|
|
|
|
Y. Jia and G. Churchward Interactions of the Integrase Protein of the Conjugative Transposon Tn916 with Its Specific DNA Binding Sites J. Bacteriol., October 1, 1999; 181(19): 6114 - 6123. [Abstract] [Full Text]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
A. Gravel, N. Messier, and P. H. Roy Point Mutations in the Integron Integrase IntI1 That Affect Recombination and/or Substrate Recognition J. Bacteriol., October 15, 1998; 180(20): 5437 - 5442. [Abstract] [Full Text]
|
|
|
|
 |
|
 M. R. Redinbo, L. Stewart, P. Kuhn, J. J. Champoux, and W. G. Hol Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with DNA Science, March 6, 1998; 279(5356): 1504 - 1513. [Abstract] [Full Text]
|
|
|
|
|
|
L. Stewart, M. R. Redinbo, X. Qiu, W. G. Hol, and J. J. Champoux A Model for the Mechanism of Human Topoisomerase I Science, March 6, 1998; 279(5356): 1534 - 1541. [Abstract] [Full Text]
|
|
|
|
|
|
A. C. Shaikh and P. D. Sadowski Trans Complementation of Variant Cre Proteins for Defects in Cleavage and Synapsis J. Biol. Chem., September 22, 2000; 275(39): 30186 - 30195. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Tribble, Y.-T. Ahn, J. Lee, T. Dandekar, and M. Jayaram DNA Recognition, Strand Selectivity, and Cleavage Mode during Integrase Family Site-specific Recombination J. Biol. Chem., July 14, 2000; 275(29): 22255 - 22267. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. I. Belova, R. Prasad, S. A. Kozyavkin, J. A. Lake, S. H. Wilson, and A. I. Slesarev A type IB topoisomerase with DNA repair activities PNAS, May 22, 2001; 98(11): 6015 - 6020. [Abstract] [Full Text] [PDF]
|
|