Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I

Journal of Molecular Biology

Volumn 370, Issue 1, 2007, Pages 157-169

  Jakubauskas, Arturas ^a   Giedriene, Jolanta ^a   Bujnicki, Janusz M ^b   Janulaitis, Arvydas ^a,c  

^a VILNIUS UNIVERSITY   (Lithuania)

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

^c Fermentas UAB   (Lithuania)

Author keywords

active site; endonuclease VII; HNH; restriction endonuclease; type IIS

Indexed keywords

RESTRICTION ENDONUCLEASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE T4; BIOINFORMATICS; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS; VALIDATION STUDY;

EID: 34249276750     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.04.049     Document Type: Article

References (46)

1. Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A., Bitinaite J., et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucl. Acids Res. 31 (2003) 1805-1812
2. Li L., Wu L.P., and Chandrasegaran S. Functional domains in Fok I restriction endonuclease. Proc. Natl Acad. Sci. USA 89 (1992) 4275-4279
3. Wah D.A., Hirsch J.A., Dorner L.F., Schildkraut I., and Aggarwal A.K. Structure of the multimodular endonuclease FokI bound to DNA. Nature 388 (1997) 97-100
4. Bitinaite J., Wah D.A., Aggarwal A.K., and Schildkraut I. FokI dimerization is required for DNA cleavage. Proc. Natl Acad. Sci. USA 95 (1998) 10570-10575
5. Zaremba M., Urbanke C., Halford S.E., and Siksnys V. Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily. J. Mol. Biol. 336 (2004) 81-92
6. Lagunavicius A., Sasnauskas G., Halford S.E., and Siksnys V. The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. J. Mol. Biol. 326 (2003) 1051-1064
7. Kriukiene E., Lubiene J., Lagunavicius A., and Lubys A. MnlI- The member of H-N-H subtype of type IIS restriction endonucleases. Biochim. Biophys. Acta 1751 (2005) 194-204
8. Kriukiene E. Domain organization and metal ion requirement of the type IIS restriction endonuclease MnlI. FEBS Letters 580 (2006) 6115-6122
9. Azarinskas A., Maneliene Z., and Jakubauskas A. Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: discovery, cloning and expression in Escherichia coli. J. Biotechnol. 123 (2006) 288-296
10. Cymerman I.A., Obarska A., Skowronek K.J., Lubys A., and Bujnicki J.M. Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins: Struct. Funct. Genet. 65 (2006) 867-876
11. Saravanan M., Bujnicki J.M., Cymerman I.A., Rao D.N., and Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res. 32 (2004) 6129-6135
12. Bath A.J., Milsom S.E., Gormley N.A., and Halford S. E. Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem. 277 (2002) 4024-4033
13. Armalyte E., Bujnicki J.M., Giedriene J., Gasiunas G., Kosinski J., and Lubys A. Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains. J. Biol. Chem. 280 (2005) 41584-41594
14. Samuelson J.C., Zhu Z., and Xu S.Y. The isolation of strand-specific nicking endonucleases from a randomized SapI expression library. Nucl. Acids Res. 32 (2004) 3661-3671
15. Zhu Z., Samuelson J.C., Zhou J., Dore A., and Xu S.Y. Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI. J. Mol. Biol. 337 (2004) 573-583
16. Butkus V., Bitinaite J., Kersulyte D., and Janulaitis A. A new restriction endonuclease Eco31I recognizing a non-palindromic sequence. Biochim. Biophys. Acta 826 (1985) 208-212
17. Bitinaite J., Mitkaite G., Dauksaite V., Jakubauskas A., Timinskas A., Vaisvila R., et al. Evolutionary relationship of Alw26I, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences. Mol. Genet. Genom. 267 (2002) 664-672
18. Marchler-Bauer A., and Bryant S.H. CD-Search: protein domain annotations on the fly. Nucl. Acids Res. 32 (2004) W327-W331
19. Bujnicki J.M., Radlinska M., and Rychlewski L. Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases. Mol. Microbiol. 37 (2000) 1280-1281
20. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. InterPro, progress and status in 2005. Nucl. Acids Res. 33 (2005) D201-D205
21. Raaijmakers H., Vix O., Toro I., Golz S., Kemper B., and Suck D. X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture. EMBO J. 18 (1999) 1447-1458
22. Li C.L., Hor L.I., Chang Z.F., Tsai L.C., Yang W.Z., and Yuan H.S. DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J. 22 (2003) 4014-4025
23. Galburt E.A., Chevalier B., Tang W., Jurica M.S., Flick K.E., Monnat Jr. R.J., and Stoddard B.L. A novel endonuclease mechanism directly visualized for I-PpoI. Nature Struct. Biol. 6 (1999) 1096-1099
24. Miller M.D., Tanner J., Alpaugh M., Benedik M.J., and Krause K.L. 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. Nature Struct. Biol. 1 (1994) 461-468
25. Cheng Y.S., Hsia K.C., Doudeva L.G., Chak K.F., and Yuan H.S. The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases. J. Mol. Biol. 324 (2002) 227-236
26. Ko T.P., Liao C.C., Ku W.Y., Chak K.F., and Yuan H. S. The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure 7 (1999) 91-102
27. Kleanthous C., Kuhlmann U.C., Pommer A.J., Ferguson N., Radford S.E., Moore G.R., et al. Structural and mechanistic basis of immunity toward endonuclease colicins. Nature Struct. Biol. 6 (1999) 243-252
28. Bujnicki J.M., Radlinska M., and Rychlewski L. Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem. Sci. 26 (2001) 9-11
29. Shen B.W., Landthaler M., Shub D.A., and Stoddard B.L. DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J. Mol. Biol. 342 (2004) 43-56
30. Mate M.J., and Kleanthous C. Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. J .Biol. Chem. 279 (2004) 34763-34769
31. Flick K.E., Jurica M.S., Monnat Jr. R.J., and Stoddard B.L. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature 394 (1998) 96-101
32. Pottmeyer S., and Kemper B. T4 endonuclease VII resolves cruciform DNA with nick and counter-nick and its activity is directed by local nucleotide sequence. J. Mol. Biol. 223 (1992) 607-615
33. Ausubel F.M., Brent R., Kingston R.E., Moore D. D., Seidman J.G., Smith J.A., and Struhl K. Editors of Current Protocols in Molecular Biology vol. 1-4 (1987), John Wiley & Sons, Inc., New York
34. Fenton C., Xu H., Petersen E.I., Petersen S.B., and el-Gewely M.R. Random mutagenesis for protein breeding. Methods Mol. Biol. 182 (2002) 231-241
35. Brons-Poulsen J., Nohr J., and Larsen L.K. Megaprimer method for polymerase chain reaction-mediated generation of specific mutations in DNA. Methods Mol. Biol. 182 (2002) 71-76
36. Whitehead P.R., and Brown N.L. A simple and rapid method for screening bacteria for type II restriction endonucleases: enzymes in Aphanothece halophytica. Arch. Microbiol. 141 (1985) 70-74
37. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
38. Combet C., Blanchet C., Geourjon C., and Deleage G. NPS@: network protein sequence analysis. Trends Biochem. Sci. 25 (2000) 147-150
39. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., et al. Pfam: clans, web tools and services. Nucl. Acids Res. 34 (2006) D247-D251
40. Letunic I., Copley R.R., Pils B., Pinkert S., Schultz J., and Bork P. SMART 5: domains in the context of genomes and networks. Nucl. Acids Res. 34 (2006) D257-D260
41. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformat. 4 (2003) 41
42. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., et al. CDD: a Conserved Domain Database for protein classification. Nucl. Acids Res. 33 (2005) D192-D196
43. Madera M., Vogel C., Kummerfeld S.K., Chothia C., and Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucl. Acids Res. 32 (2004) D235-D239
44. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (2005) 951-960
45. Kurowski M.A., and Bujnicki J.M. GeneSilico protein structure prediction meta-server. Nucl. Acids Res. 31 (2003) 3305-3307
46. Kosinski J., Cymerman I.A., Feder M., Kurowski M. A., Sasin J.M., and Bujnicki J.M. 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: Struct. Funct. Genet. 53 Suppl. 6 (2003) 369-379