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PMID: 3011407 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

The integrase family of site-specific recombinases: regional similarities and global diversity.

The EMBO journal ·Vol. 5 ·No. 2 ·1986-02-00 ·Pages 433-40

Argos P, Landy A, Abremski K, Egan JB, Haggard-Ljungquist E, Hoess RH, Kahn ML, Kalionis B, Narayana SV, Pierson LS

Abstract

A combination of two methods for detecting distant relationships in protein primary sequences was used to compare the site-specific recombination proteins encoded by bacteriophage lambda, phi 80, P22, P2, 186, P4 and P1. This group of proteins exhibits an unexpectedly large diversity of sequences. Despite this diversity, all of the recombinases can be aligned in their C-terminal halves. A 40-residue region near the C terminus is particularly well conserved in all the proteins and is homologous to a region near the C terminus of the yeast 2 mu plasmid Flp protein. This family of recombinases does not appear to be related to any other site-specific recombinases. Three positions are perfectly conserved within this family: histidine, arginine and tyrosine are found at respective alignment positions 396, 399 and 433 within the well-conserved C-terminal region. We speculate that these residues contribute to the active site of this family of recombinases, and suggest that tyrosine-433 forms a transient covalent linkage to DNA during strand cleavage and rejoining.

MeSH Terms
Amino Acid Sequence Bacteriophage lambda/enzymology Coliphages/enzymology DNA Helicases/genetics DNA Nucleotidyltransferases/genetics Integrases Protein Conformation Species Specificity
Chemicals
DNA Nucleotidyltransferases Integrases DNA Helicases
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Argos P
Landy A
Abremski K
Egan J B
Haggard-Ljungquist E
Hoess R H
Kahn M L
Kalionis B
Narayana S V
Pierson L S
References (63)
63 references, click to expand
  1. Attachment of prophage P2: gene order at different host chromosomal sites.
    Virology. 1969 Dec;39(4):867-81 PMID: 4902260
  2. Bacteriophage P1 Cre-loxP site-specific recombination. Site-specific DNA topoisomerase activity of the Cre recombination protein.
    J Biol Chem. 1986 Jan 5;261(1):391-6 PMID: 3001054
  3. Genetics of P2 and related phages.
    Adv Genet. 1971;16:199-237 PMID: 4947104
  4. Excision-deficient mutants of bacteriophage P2.
    Virology. 1972 Jul;49(1):180-7 PMID: 4556923
  5. Integration stie of noninducible coliphage 186.
    J Bacteriol. 1972 Aug;111(2):303-7 PMID: 4559723
  6. Bacteriophage P4: a satellite virus depending on a helper such as prophage P2.
    Virology. 1973 Feb;51(2):327-44 PMID: 4571379
  7. Integrative recombination of bacteriophage lambda DNA in vitro.
    Proc Natl Acad Sci U S A. 1975 Mar;72(3):1072-6 PMID: 1055366
  8. An assessment of protein secondary structure prediction methods based on amino acid sequence.
    Biochim Biophys Acta. 1976 Aug 9;439(2):261-73 PMID: 952963
  9. Specialized transduction by bacteriophage P22 in Salmonella typhimurium: genetic and physical structure of the transducing genomes and the prophage attachment site.
    Genetics. 1976 Jul;83(3 PT.2):433-58 PMID: 783004
  10. Specialized transducing phages derived from phage P22 that carry the pro AB region of the host, Salmonella typhimurium: genetic evidence for their structure and mode of transduction.
    Genetics. 1976 Jul;83(3 PT.2):459-75 PMID: 783005
  11. Strand breakage by the DNA untwisting enzyme results in covalent attachment of the enzyme to DNA.
    Proc Natl Acad Sci U S A. 1977 Sep;74(9):3800-4 PMID: 198805
  12. Nicking-closing activity associated with bacteriophage lambda int gene product.
    Proc Natl Acad Sci U S A. 1979 Aug;76(8):3760-4 PMID: 226979
  13. Water, protein folding, and the genetic code.
    Science. 1979 Nov 2;206(4418):575-7 PMID: 493962
  14. Interaction of int protein with specific sites on lambda att DNA.
    Cell. 1979 Oct;18(2):297-307 PMID: 159130
  15. The lambda phage att site: functional limits and interaction with Int protein.
    Nature. 1980 May 8;285(5760):85-91 PMID: 6246439
  16. Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA.
    J Biol Chem. 1980 Jun 25;255(12):5560-5 PMID: 6155377
  17. Site-specific recombination functions of bacteriophage lambda: DNA sequence of regulatory regions and overlapping structural genes for Int and Xis.
    Proc Natl Acad Sci U S A. 1980 May;77(5):2482-6 PMID: 6446713
  18. Nucleotide sequence of the yeast plasmid.
    Nature. 1980 Aug 28;286(5776):860-5 PMID: 6251374
  19. DNA sequence of the int-xis-Pi region of the bacteriophage lambda; overlap of the int and xis genes.
    Nucleic Acids Res. 1980 Apr 25;8(8):1765-82 PMID: 6253947
  20. Purification and properties of the Escherichia coli protein factor required for lambda integrative recombination.
    J Biol Chem. 1981 Sep 10;256(17):9246-53 PMID: 6267068
  21. Lysogenization by satellite phage P4.
    Virology. 1981 Aug;113(1):20-38 PMID: 7023020
  22. Protein folding.
    Annu Rev Biochem. 1981;50:497-532 PMID: 7023364
  23. Transposon-mediated site-specific recombination in vitro: DNA cleavage and protein-DNA linkage at the recombination site.
    Cell. 1981 Sep;25(3):721-8 PMID: 6269756
  24. A novel role for site-specific recombination in maintenance of bacterial replicons.
    Cell. 1981 Sep;25(3):729-36 PMID: 7026049
  25. Structure and function of the phage lambda att site: size, int-binding sites, and location of the crossover point.
    Cold Spring Harb Symp Quant Biol. 1981;45 Pt 1:429-37 PMID: 6457725
  26. Transposon-specified site-specific recombination.
    Proc Natl Acad Sci U S A. 1982 Jan;79(1):46-50 PMID: 6275390
  27. Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites.
    J Mol Biol. 1981 Aug 25;150(4):467-86 PMID: 6276557
  28. An examination of the expected degree of sequence similarity that might arise in proteins that have converged to similar conformational states. The impact of such expectations on the search for homology between the structurally similar domains of rhodanese.
    J Mol Biol. 1981 Sep 5;151(1):179-97 PMID: 6948967
  29. Inheritance of prophage P2 in bacterial crosses.
    Virology. 1958 Oct;6(2):357-81 PMID: 13593178
  30. Specialized transduction of tryptophan markers in Escherichia coli K12 by bacteriophage phi-80.
    Virology. 1963 Apr;19:475-82 PMID: 13933810
  31. Integration and excision of bacteriophage lambda: the mechanism of conservation site specific recombination.
    Annu Rev Genet. 1981;15:143-67 PMID: 6461289
  32. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.
    Nucleic Acids Res. 1982 May 11;10(9):2951-61 PMID: 7099970
  33. Amino acid distribution in protein secondary structures.
    Int J Pept Protein Res. 1982 Apr;19(4):380-93 PMID: 7118408
  34. Nucleotide sequence of gamma delta resolvase gene and demonstration that its gene product acts as a repressor of transcription.
    Nature. 1982 Nov 25;300(5890):381-3 PMID: 6292730
  35. Bacteriophage lambda int protein recognizes two classes of sequence in the phage att site: characterization of arm-type sites.
    Proc Natl Acad Sci U S A. 1982 Dec;79(24):7724-8 PMID: 6218502
  36. Genetic map of coliphage 186 from a novel use of marker rescue frequencies.
    Mol Gen Genet. 1982;187(1):87-95 PMID: 6962313
  37. Studies on the properties of P1 site-specific recombination: evidence for topologically unlinked products following recombination.
    Cell. 1983 Apr;32(4):1301-11 PMID: 6220808
  38. Site-specific relaxation and recombination by the Tn3 resolvase: recognition of the DNA path between oriented res sites.
    Cell. 1983 Apr;32(4):1313-24 PMID: 6301692
  39. A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases.
    J Biol Chem. 1983 May 25;258(10):6450-7 PMID: 6343377
  40. DNA inversions in the chromosome of Escherichia coli and in bacteriophage Mu: relationship to other site-specific recombination systems.
    Proc Natl Acad Sci U S A. 1983 Sep;80(17):5355-8 PMID: 6310572
  41. Sequence of the site-specific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1.
    EMBO J. 1983;2(10):1733-40 PMID: 6315399
  42. The mechanism of phage lambda site-specific recombination: site-specific breakage of DNA by Int topoisomerase.
    Cell. 1983 Dec;35(3 Pt 2):795-803 PMID: 6317202
  43. Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein.
    J Biol Chem. 1984 Feb 10;259(3):1509-14 PMID: 6319400
  44. Identification of the breakage-reunion subunit of T4 DNA topoisomerase.
    J Biol Chem. 1984 Jul 25;259(14):9177-81 PMID: 6086624
  45. Patterns of lambda Int recognition in the regions of strand exchange.
    Cell. 1983 May;33(1):261-72 PMID: 6235918
  46. Cloning of the integration and attachment regions of bacteriophage P4.
    Mol Gen Genet. 1984;195(1-2):44-51 PMID: 6092863
  47. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase.
    J Biol Chem. 1985 Mar 25;260(6):3350-4 PMID: 2982857
  48. Interaction of the lambda site-specific recombination protein Xis with attachment site DNA.
    Proc Natl Acad Sci U S A. 1985 Feb;82(4):1040-4 PMID: 3156374
  49. Resolvase-mediated recombination intermediates contain a serine residue covalently linked to DNA.
    Cold Spring Harb Symp Quant Biol. 1984;49:245-9 PMID: 6099239
  50. Comparative analysis of invertible DNA in phage genomes.
    Cold Spring Harb Symp Quant Biol. 1984;49:301-11 PMID: 6241552
  51. Components of the site-specific recombination system encoded by the yeast plasmid 2-micron circle.
    Cold Spring Harb Symp Quant Biol. 1984;49:779-87 PMID: 6397322
  52. In vitro systems for genetic recombination of the DNAs of bacteriophage T7 and yeast 2-micron circle.
    Cold Spring Harb Symp Quant Biol. 1984;49:789-96 PMID: 6597764
  53. Site-specific genetic recombination promoted by the FLP protein of the yeast 2-micron plasmid in vitro.
    Cold Spring Harb Symp Quant Biol. 1984;49:797-804 PMID: 6597765
  54. The phi 80 and P22 attachment sites. Primary structure and interaction with Escherichia coli integration host factor.
    J Biol Chem. 1985 Apr 10;260(7):4468-77 PMID: 2984205
  55. Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system.
    J Mol Biol. 1985 Feb 5;181(3):351-62 PMID: 3856690
  56. The FLP recombinase of the 2 micron circle DNA of yeast: interaction with its target sequences.
    Cell. 1985 Apr;40(4):795-803 PMID: 3879971
  57. Evidence for a repeating domain in type I restriction enzymes.
    EMBO J. 1985 May;4(5):1351-5 PMID: 2988943
  58. The FLP protein of the 2-micron plasmid of yeast. Purification of the protein from Escherichia coli cells expressing the cloned FLP gene.
    J Biol Chem. 1985 Oct 5;260(22):12313-9 PMID: 2995370
  59. Determination of DNA sequences essential for FLP-mediated recombination by a novel method.
    J Biol Chem. 1985 Oct 5;260(22):12320-7 PMID: 2995371
  60. The FLP protein of the 2-micron plasmid of yeast. Inter- and intramolecular reactions.
    J Biol Chem. 1985 Oct 5;260(22):12328-35 PMID: 3900073
  61. Generation of single base-pair deletions, insertions, and substitutions by a site-specific recombination system.
    Proc Natl Acad Sci U S A. 1985 Oct;82(20):6990-4 PMID: 2995999
  62. Control of directionality in lambda site specific recombination.
    Science. 1985 Nov 22;230(4728):906-11 PMID: 2932798
  63. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 .
    J Mol Biol. 1971 Oct 28;61(2):409-24 PMID: 5167087
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1986-02-00
Pages
433-40
Language
English
Region
England
NLM ID
8208664
PMCID
PMC1166749
Subset
IM
Grants
NIAID NIH HHS · AI 13544 · United States
External Links
PubMed source PMC Full Text View journal details
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