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Fig. 4 | Mobile DNA

Fig. 4

From: Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8

Fig. 4

Structure based alignments of linker and RLE regions. a Multiple sequence alignment and Ali2D prediction of the most conserved region of the linker. The Ali2D predicted secondary for R2Bm protein are marked above the R2Bm sequence. The canonical ββα structure of a gag-knuckle/IAP is also presented. The secondary structure of Prp8 is given below the Prp8 sequences. The Prp8 secondary structures are from several reported crystal and cryo-EM structures: 3JCM, 5LJ3, 4i43B. Rounded bars are α-helices and arrows are β-strands. b Multiple sequence alignment RLE from LINEs, type II restriction enzymes, archeal Holliday junction resolvases, influenza PA endonuclease, and Prp8. Abbreviations: R2Bm = Bombyx mori (M16558.1); R2Lp = Limulus polyphemus (AF015814.1); R2Dr = Danio rario (34392533); R8Hm = Hydra magnipapillata; R9Av = Adenata vaga (ACV95454.1); R4Pe = Parascaris equorum (AAB02297.1); DongFr = Fugu rubripes; CRE2Cf = Crithidia fasciculata; ZARTc = Trypanosoma cruzi; HERODr = Danio rario; HEROBf = Branchiostoma floridae; NeSLTv = Trichomonas vaginalis; NeSLAc = Acanthamoeba castellanii; UtopAm = Alligator mississippiensis Utopia; UtopCp = Crocodylus porosus Utopia; Prp8Hs = Homo sapiens (NP_006436.3); Prp8Dm = Drosophila melangaster (NP_610735.1); Prp8At = Arabidopsis thaliana (Q9T0I6); Prp8Sc = Saccharomyces cerevisiae (P33334); Prp8Sp = Schizosaccharomyces pombe (O14187); PA En = Influenza virus PA endonclease (3HW4). R8Hm, DongFr, CRE2Cf, CZARTc, HERODr, HEROBf, NeSLTv, NeSLAc, UtopAm, and UtopCp sequences were collected from Repbase [69]. Holiday junction resolvases Ssol Hje (1ob8) and Ssol Hjc (1hh1) are from Sulfolobus solfataricus. Holiday junction resolvase Stok Hjc (2eo0) is from Sulfolobus tokodaii str. 7 Pfur Hjc (1gef) is from Pyrococcus furiosus

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