Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Feder, Marcin ^a   Bujnicki, Janusz M ^a  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE; LYSINE; NUCLEASE;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; CYANOBACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; GLOEOBACTER VIOLACEUS PCC 7421; THERMUS THERMOPHILUS;

EID: 25444501004     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-21     Document Type: Article

References (78)

1. Aggarwal AK: Structure and function of restriction endonucleases. CurrOpinStructBiol 1995, 5:11-19.
2. Bujnicki JM: Molecular phylogenetics of restriction endonucleases. In Restriction Endonucleases Volume 14. Edited by: Pingoud A. Berlin, Springer-Verlag; 2004:63-87.
3. Kovall RA, Matthews BW: Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases. Proc Natl Acad Sci U S A 1998, 95:7893-7897.
4. Ban C, Yang W: Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. Embo J 1998, 17:1526-1534.
5. Tsutakawa SE, Muto T, Kawate T, Jingami H, Kunishima N, Ariyoshi M, Kohda D, Nakagawa M, Morikawa K: Crystallographic and functional studies of very short patch repair endonuclease. Mol Cell 1999, 3:621-628.
6. Hickman AB, Li Y, Mathew SV, May EW, Craig NL, Dyda F: Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol Cell 2000, 5:1025-1034.
7. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K: Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure (Camb) 2001, 9:197-204.
8. Bond CS, Kvaratskhelia M, Richard D, White MF, Hunter WN: Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus. Proc Natl Acad Sci U S A 2001, 98:5509-5514.
9. Middleton CL, Parker JL, Richard DJ, White MF, Bond CS: Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje. Nucleic Acids Res 2004, 32:5442-5451.
10. Hadden JM, Convery MA, Declais AC, Lilley DM, Phillips SE: Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I. Nat Struct Biol 2001, 8:62-67.
11. Nishino T, Komori K, Ishino Y, Morikawa K: X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes. Structure (Camb) 2003, 11:445-457.
12. Venclovas C, Timinskas A, Siksnys V: Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV. Proteins 1994, 20:279-282.
13. Pingoud A: Restriction endonucleases. In Nucleic Acids and Molecular Biology Volume 14. Edited by: Gross HJ. Berlin, Heidelberg, Springer-Verlag; 2004:442.
14. Kovall RA, Matthews BW: Type II restriction endonucleases: structural, functional and evolutionary relationships. Curr Opin Chem Biol 1999, 3:578-583.
15. Horton JR, Blumenthal RM, Cheng X: Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in the DNA cleavage. In Restriction endonucleases Volume 14. Edited by: Pingoud AM. Berlin, Springer-Verlag; 2004:361-392.
16. Skirgaila R, Grazulis S, Bozic D, Huber R, Siksnys V: Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. J Mol Biol 1998, 279:473-481.
17. Bujnicki JM, Rychlewski L: Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Gene 2001, 267:183-191.
18. Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A: Evolutionary relationship between different subgroups of restriction endonucleases. J Biol Chem 2002, 277:14306-14314.
19. Tamulaitis G, Solonin AS, Siksnys V: Alternative arrangements of catalytic residues at the active sites of restriction enzymes. FEBS Lett 2002, 518:17-22.
20. Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK: Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature 1994, 368:660-664.
21. Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK: Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat Struct Biol 2000, 7:134-140.
22. Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Luder G, Morgan R, Kubareva E, Pingoud A: Specificity changes in the evolution of Type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J Biol Chem 2004.
23. Bujnicki JM, Rychlewski L: Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases. Protein Sci 2001, 10:656-660.
24. Li H, Trotta CR, Abelson J: Crystal structure and evolution of a transfer RNA splicing enzyme. Science 1998, 280:279-284.
25. Todone F, Weinzierl RO, Brick P, Onesti S: Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc Natl Acad Sci U S A 2000, 97:6306-6310.
26. Daiyasu H, Komori K, Sakae S, Ishino Y, Toh H: Hjc resolvase is a distantly related member of the type II restriction endonuclease family. Nucleic Acids Res 2000, 28:4540-4543.
27. Kvaratskhelia M, Wardleworth BN, Norman DG, White MF: A conserved nuclease domain in the archaeal Holliday junction resolving enzyme Hjc. J Biol Chem 2000, 275:25540-25546.
28. Aravind L, Makarova KS, Koonin EV: SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 2000, 28:3417-3432.
29. Bujnicki JM, Rychlewski L: Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J Mol Microbiol Biotechnol 2001, 3:69-72.
30. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
31. Bujnicki JM: Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Curr Protein Pept Sci 2003, 4:327-337.
32. Godzik A: Fold recognition methods. Methods Biochem Anal 2003, 44:525-546.
33. Kurowski MA, Bujnicki JM: GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003, 31:3305-3307.
34. Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM: A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 2003, 53 Suppl 6:369-379.
35. Lundstrom J, Rychlewski L, Bujnicki JM, Elofsson A: Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10:2354-2362.
36. Fuxreiter M, Simon I: Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases. Protein Sci 2002, 11:1978-1983.
37. Simons KT, Kooperberg C, Huang E, Baker D: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997, 268:209-225.
38. Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Luder G, Xu SY, Pingoud A: PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J Mol Biol 2003, 329:913-929.
39. Nakamura Y, Kaneko T, Sato S, Mimuro M, Miyashita H, Tsuchiya T, Sasamoto S, Watanabe A, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Nakazaki N, Shimpo S, Takeuchi C, Yamada M, Tabata S: Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. DNA Res 2003, 10:137-145.
40. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO: Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
41. Lambowitz AM, Belfort M: Introns as mobile genetic elements. Annu Rev Biochem 1993, 62:587-622.
42. Mahillon J, Leonard C, Chandler M: IS elements as constituents of bacterial genomes. Res Microbiol 1999, 150:675-687.
43. Sadykov M, Asami Y, Niki H, Handa N, Itaya M, Tanokura M, Kobayashi I: Multiplication of a restriction-modification gene complex. Mol Microbiol 2003, 48:417-427.
44. Gimble FS: Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol Lett 2000, 185:99-107.
45. Chinen A, Uchiyama I, Kobayashi I: Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 2000, 259:109-121.
46. Kobayashi I: Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 2001, 29:3742-3756.
47. Handa N, Nakayama Y, Sadykov M, Kobayashi I: Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex. Mol Microbiol 2001, 40:932-940.
48. Jurica MS, Stoddard BL: Homing endonucleases: structure, function and evolution. Cell Mol Life Sci 1999, 55:1304-1326.
49. Mahdi AA, Sharples GJ, Mandal TN, Lloyd RG: Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J Mol Biol 1996, 257:561-573.
50. Lyra C, Halme T, Torsti AM, Tenkanen T, Sivonen K: Site-specific restriction endonucleases in cyanobacteria. J Appl Microbiol 2000, 89:979-991.
51. Matveyev AV, Young KT, Meng A, Elhai J: DNA methyltransferases of the cyanobacterium Anabaena PCC 7120. Nucleic Acids Res 2001, 29:1491-1506.
52. Muro-Pastor AM, Flores E, Herrero A, Wolk CP: Identification, genetic analysis and characterization of a sugar-non-specific nuclease from the cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol 1992, 6:3021-3030.
53. Takahashi I, Hayano D, Asayama M, Masahiro F, Watahiki M, Shirai M: Restriction barrier composed of an extracellular nuclease and restriction endonuclease in the unicellular cyanobacterium Microcystis sp. FEMS Microbiol Lett 1996, 145:107-111.
54. Jeltsch A: Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems? Gene 2003, 317:13-16.
55. Carr NG, Mann NH: The oceanic cyanobacterial picoplankton. In The molecular biology of Cyanobacteria Edited by: Bryant DA. Dordrecht, Kluwer Academic Publishers; 1994.
56. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. NucleicAcidsRes 1997, 25:3389-3402.
57. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
58. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
59. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
60. Chapman B, Chang J: Biopython: python tools for computational biology. ACM SIGBIO Newslett 2000, 20:15-19.
61. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH: CDD: acurated Entrez database of conserved domain alignments. Nucleic Acids Res 2003, 31:383-387.
62. McGuffin LJ, Bryson K, Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405.
63. Rost B, Yachdav G, Liu J: The PredictProtein server. Nucleic Acids Res 2004, 32:W321-6.
64. Ouali M, King RD: Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000, 9:1162-1176.
65. Adamczak R, Porollo A, Meller J: Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 2004, 56:753-767.
66. Cuff JA, Barton GJ: Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000, 40:502-511.
67. Meiler J, Baker D: Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci U S A 2003, 100:12105-12110.
68. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R: Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003, 53 Suppl 6:491-496.
69. Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9:232-241.
70. Kelley LA, MacCallum RM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000, 299:499-520.
71. Fischer D: Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pacific Symp Biocomp 2000:119-130.
72. Shi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310:243-257.
73. Jones DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287:797-815.
74. Zhou H, Zhou Y: Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004, 55:1005-1013.
75. Luthy R, Bowie JU, Eisenberg D: Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
76. Sasin JM, Bujnicki JM: COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004, 32:W586-9.
77. Holm L, Sander C: Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-138.
78. Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R: Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol 2000, 7:792-799.