Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW Mol Cell Biol. 2008 The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P J Mol Biol. 2008 YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S RNA. 2008 MetaMQAP: a meta-server for the quality assessment of protein models. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM BMC Bioinformatics. 2008 Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J J Mol Biol. 2008 HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG J Mol Biol. 2008 YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962 Purta E, O\'Connor M, Bujnicki JM, Douthwaite S J Mol Biol. 2008 IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis. Gyrd-Hansen M, Darding M, Miasari M, Santoro MM, Zender L, Xue W, Tenev T, da Fonseca PC, Zvelebil M, Bujnicki JM, Lowe S, Silke J, Meier P Nat Cell Biol. 2008 Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr. Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A Biochem Biophys Res Commun. 2008 The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA Mol Cell Biol. 2007 Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM BMC Bioinformatics. 2007 Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J Nucleic Acids Res. 2007 Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species. Schäfer P, Cymerman IA, Bujnicki JM, Meiss G Protein Sci. 2007 SURF'S UP! - protein classification by surface comparisons Sasin JM, Godzik A, Bujnicki JM J Biosci. 2007 Transcriptome profile of human colorectal adenomas. Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G Mol Cancer Res. 2007 PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Pietal MJ, Tuszynska I, Bujnicki JM Bioinformatics. 2007 Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Pena V, Liu S, Bujnicki JM, Lührmann R, Wahl MC Mol Cell. 2007 Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Ozanick SG, Bujnicki JM, Sem DS, Anderson JT Nucleic Acids Res. 2007 I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition Orlowski J, Boniecki M, Bujnicki JM Bioinformatics. 2007 Novel protein fold discovered in the PabI family of restriction enzymes. Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I Nucleic Acids Res. 2007 Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL PLoS One. 2007 [Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling]. Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES Mol Biol (Mosk). 2007 A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering. Kosinski J, Kubareva E, Bujnicki JM Proteins. 2007 Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics. Koscinski L, Feder M, Bujnicki JM Cell Cycle. 2007 Identification of a single HNH active site in type IIS restriction endonuclease Eco31I Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A J Mol Biol. 2007 Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, Den\'mukhamedov MM, Melnik BS, Kolinski A, Gront D, Feder M, Solonin AS, Bujnicki JM BMC Struct Biol. 2007 Phylogenetic analysis of haloalkane dehalogenases. Chovancová E, Kosinski J, Bujnicki JM, Damborský J Proteins. 2007 Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L Nucleic Acids Res. 2006 Complete cap 4 formation is not required for viability in Trypanosoma brucei. Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA Eukaryot Cell. 2006 Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. Tkaczuk KL, Obarska A, Bujnicki JM BMC Evol Biol. 2006