References

Aravind L, Walker DR, Koonin EV (1999) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res 27:1223-1242 Belfort M, Perlman PS (1995) Mechanisms of intron mobility. J Biol Chem 270:3023730240

Belfort M, Derbyshire V, Cousineau B, Lambowitz A (2002) Mobile introns: pathways and proteins. In: Craig N, Craigie R, Gellert M, Lambowitz A (eds) Mobile DNA II. ASM Press, Washington, DC, pp 761-783 Belle A, Landthaler M, Shub DA (2002) Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev 16:351-362 Bryk M, Quirk SM, Mueller JE, Loizos N, Lawrence C, Belfort M (1993) The td intron endonuclease makes extensive sequence tolerant contacts across the minor groove of its DNA target. EMBO J 12:2141-2149 BrykM,Belisle M, Mueller JE, Belfort M (1995) Selection of a remote cleavage site by l-TevI, the td intron-encoded endonuclease. J Mol Biol 247:197-210 Bujnicki JM, Radlinska M, Rychlewski L (2001) Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem Sci 26:9-11

Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA (2001) Structural mechanism for rifamycin inhibition of bacterial DNA polymerase. Cell 104:901-912

Cummings DJ, Michel F, McNally KL (1989) DNA sequence analysis of the 24.5 kilobase pair cytochrome oxidase subunit I mitochondrial gene from Podospora anserina: a gene with sixteen introns. Curr Genet 16:381-406 Dean AB, Stanger MJ, Dansereau JT, Van Roey P, Derbyshire V, Belfort M (2002) Zinc finger as distance determinant in the flexible linker of intron endonuclease I-Tevl. Proc Natl Acad Sci USA 99:8554-8561 Derbyshire V, Kowalski JC, Dansereau JT, Hauer CR, Belfort M (1997) Two-domain structure of the td intron-encoded endonuclease I-Tevl correlates with the two-domain configuration of the homing site. J Mol Biol 265:494-506 Edgell DR, Shub DA (2001) Related homing endonucleases I-Bmol and I-Tevl use different strategies to cleave homologous recognition sites. Proc Natl Acad Sci USA 98:78987903

Edgell DR, Derbyshire V, van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M (2004a) Intron endonuclease I-Tevl also functions as a transcriptional auto-repressor. Nat Struct Mol Biol 11:936-944

Edgell DR, Stanger MJ, Belfort M (2004b) Coincidence of cleavage sites of intron endonu-clease I-TevI and critical sequences of the host thymidylate synthase gene. J Mol Biol 343:1231-1241

Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL (1999) A novel endonuclease mechanism directly visualized for I-Ppol. Nat Struct Biol 6:10961099

Gott JM, Zeeh A, Bell-Pedersen D, Ehrenman K, Belfort M, Shub DA (1988) Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside. Genes Dev 2:1791-1799 Henikoff S, Henikoff JG, Alford WJ, Pietrokovski S (1995) Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163:17-26 Kadyrov FA, Shlyapnikov MG, Kryukov VM (1997) A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages. FEBS Lett 415:75-80 Kowalski JC, Belfort M, Stapleton MA, Holpert M, Dansereau JT, Pietrokovski S, Baxter SM, Derbyshire V (1999) Configuration of the catalytic domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. Nucleic Acids Res 27:2115-2125

Kuhlmann UC, Moore GR, James R, Kleanthous C, Hemmings AM (1999) Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined? FEBS Lett 463:1-2 Lin J-J, Sancar A (1992) Active site of (A)BC excinuclease. I. Evidence for 5' incision by UvrC through a catalytic site involving Asp399, Asp438, Asp466 and His538 residues. J Biol Chem 267:17688-17692 Liu Q, Belle A, Shub DA, Belfort M, Edgell DR (2003) SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site. J Mol Biol 334:13-23

Michel F, Dujon B (1986) Genetic exchanges between bacteriophage T4 and filamentous fungi? Cell 46:323

Moolenaar GF, Uiterkamp RS, Zwijnenburg DA, Goosen N (1998) The C-terminal region of the Escherichia coli UvrC protein, which is homologous to the C-terminal region of the human ERCC1 protien, is involved in DNA binding and 5'-incision. Nucleic Acids Res 26:462-468

Moolenaar GF, van Rossum-Fikkert S, van Kesteren M, Goosen N (2002) Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair. Proc Natl Acad Sci USA 99:1467-1472

Mueller JE, Smith D, Bryk M, Belfort M (1995) Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site. EMBO J 14:5724-5735 Sancar A (1996) DNA excision repair. Annu Rev Biochem 65:43-81

Schneider TD, Stephens RM (1990) Sequence logos a new way to display consensus sequences. Nucleic Acids Res 18:6097-6100 Sharma M, Hinton DM (1994) Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns. J Bacteriol 176:6439-6448 Sharma M, Ellis RL, Hinton DM (1992) Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Proc Natl Acad Sci USA 89:6658-6662 Shen BW, Landthaler M, Shub DA, Stoddard BL (2004) DNA binding and cleavage by the HNH homing endonuclease I-Hmul. J Mol Biol 342:43-56

Sitbon E, Pietrokovski S (2003) New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem Sci 28:473-477 Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V (2001) Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. EMBO J 20:3631-3637

Van Roey P, Meehan L, Kowalski J, Belfort M, Derbyshire V (2002) Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat Struct Biol 9:806-811

Verhoeven EEA, van Kesteren M, Moolenaar GF, Visse R, Goosen N (2000) Catalytic sites for 3' and 5' incision of Escherichia coli nucleotide excision repair are both located in UvrC. J Biol Chem 275:5120-5123 Volff J-N, Hornung U, Schartl M (2001) Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements. Mol Genet Genom 265:711-720

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