MetaMQAP: A meta-server for the quality assessment of protein models (2008)
Pawlowski, Marcin, Gajda, Michal J, Matlak, Ryszard, Bujnicki, Janusz M
Abstract Background Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on the degree of these...
Vasu, Kommireddy, Saravanan, Matheshwaran, Bujnicki, Janusz M, Nagaraja, Valakunja
Restriction endonuclease (REase) R.KpnI from Klebsiella pneumoniae is a homodimeric enzyme, which recognizes palindromic sequence GGTAC|C and cleaves generating 4 base 3′ end overhangs. R.KpnI...
Vasu, Kommireddy, Saravanan, Matheshwaran, Bujnicki, Janusz M, Nagaraja, Valakunja
Restriction endonuclease (REase) R.KpnI from Klebsiella pneumoniae is a homodimeric enzyme, which recognizes palindromic sequence GGTAC|C and cleaves generating 4 base 3′ end overhangs. R.KpnI...
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily (2007)
Ibryashkina, Elena M, Zakharova, Marina V, Baskunov, Vladimir B, Bogdanova, Ekaterina S, Nagornykh, Maxim O, Den'mukhamedov, Marat M, ...
Abstract Background The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures have been also...
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases (2007)
Tkaczuk, Karolina L, Dunin-Horkawicz, Stanislaw, Purta, Elzbieta, Bujnicki, Janusz M
Abstract Background SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In...
The yfhQgene of Escherichia coliencodes a tRNA:Cm32/Um32 methyltransferase (2006)
Purta, Elzbieta, Van Vliet, Françoise, Tkaczuk, Karolina L, Dunin-Horkawicz, Stanislaw, Mori, Hirotada, Droogmans, Louis, ...
Abstract Background Naturally occurring tRNAs contain numerous modified nucleosides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process. In...
Phylogenomic analysis of the GIY-YIG nuclease superfamily (2006)
Dunin-Horkawicz, Stanislaw, Feder, Marcin, Bujnicki, Janusz M
Abstract Background The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons)...
Tkaczuk, Karolina L, Obarska, Agnieszka, Bujnicki, Janusz M
Abstract Background Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from...
Kosinski, Jan, Feder, Marcin, Bujnicki, Janusz M
Abstract Background The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the...
Feder, Marcin, Bujnicki, Janusz M
Abstract Background Prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the...
A homology model of restriction endonuclease SfiI in complex with DNA (2005)
Chmiel, Agnieszka A, Bujnicki, Janusz M, Skowronek, Krzysztof J
Abstract Background Restriction enzymes (REases) are commercial reagents commonly used in recombinant DNA technologies. They are attractive models for studying protein-DNA interactions and valuable...
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily (2004)
Saravanan, Matheshwaran, Bujnicki, Janusz M, Cymerman, Iwona A, Rao, Desirazu N, Nagaraja, Valakunja
The restriction endonuclease (REase) R.KpnI is an orthodox Type IIP enzyme, which binds to DNA in the absence of metal ions and cleaves the DNA sequence 5'-GGTAC^C-3' in the presence of Mg2+ as...
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily (2004)
Saravanan, Matheshwaran, Bujnicki, Janusz M, Cymerman, Iwona A, Rao, Desirazu N, Nagaraja, Valakunja
The restriction endonuclease (REase) R.KpnI is an orthodox Type IIP enzyme, which binds to DNA in the absence of metal ions and cleaves the DNA sequence 5'-GGTAC^C-3' in the presence of Mg2+ as...
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB (2003)
Kurowski, Michal A, Bhagwat, Ashok S, Papaj, Grzegorz, Bujnicki, Janusz M
Abstract Background Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB...
Pingoud,Vera, Conzelmann,Charlotte, Kinzebach,Steffen, Sudina,Anna, Metelev,Valerie, Kubareva,Elena, ...
We present here the first detailed biochemical analysis of an archaeal restriction enzyme. PspGI shows sequence similarity to SsoII, EcoRII, NgoMIV and Cfr10I, which recognize related DNA sequences....
Bmc Bioinformatics, Janusz M Bujnicki, Leszek Rychlewski
Background: Escherichia coli guanine-N2 (m 2 G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a...
Bmc Bioinformatics, Michal A Kurowski, Joanna M Sasin, Marcin Feder, Janusz Debski, Janusz M Bujnicki
Background: There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has...
Kurowski, Michal A, Sasin, Joanna M, Feder, Marcin, Debski, Janusz, Bujnicki, Janusz M
Abstract Background There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily...
Pingoud, Vera, Conzelmann, Charlotte, Kinzebach, Steffen, Sudina, Anna, Metelev, Valerie, Kubareva, Elena, ...
We present here the first detailed biochemical analysis of an archaeal restriction enzyme. PspGI shows sequence similarity to SsoII, EcoRII, NgoMIV and Cfr10I, which recognize related DNA sequences....
Sequence permutations in the molecular evolution of DNA methyltransferases (2002)
Background: DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic...
Bujnicki, Janusz M, Rychlewski, Leszek
Abstract Background Escherichia coli guanine-N2 (m 2 G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus...
Sequence permutations in the molecular evolution of DNA methyltransferases (2002)
Abstract Background DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the...
Bujnicki, Janusz M, Rychlewski, Leszek
Abstract Background The reovirus λ2 protein catalyzes mRNA capping, that is, addition of a guanosine to the 5' end of each transcript in a 5'-to-5' orientation, as well as transfer of a methyl group...
Bujnicki, Janusz M, Feder, Marcin, Radlinska, Monika, Rychlewski, Leszek
Abstract Background The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for...
Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop
Pintard, Lionel, Lecointe, François, Bujnicki, Janusz M., Bonnerot, Claire, Grosjean, Henri, Lapeyre, Bruno
The genome of Saccharomyces cerevisiae encodes three close homologues of the Escherichia coli 2′-O-rRNA methyltransferase FtsJ/RrmJ, designated Trm7p, Spb1p and Mrm2p. We present evidence that...
MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase
Pintard, Lionel, Bujnicki, Janusz M., Lapeyre, Bruno, Bonnerot, Claire
Mitochondria of the yeast Saccharomyces cerevisiae assemble their ribosomes from ribosomal proteins, encoded by the nuclear genome (with one exception), and rRNAs of 15S and 21S, encoded by the...
Droogmans, Louis, Roovers, Martine, Bujnicki, Janusz M., Tricot, Catherine, Hartsch, Thomas, Stalon, Victor, ...
N1-methyladenosine (m1A) is found at position 58 in the T-loop of many tRNAs. In yeast, the formation of this modified nucleoside is catalyzed by the essential tRNA (m1A58) methyltransferase, a...
The yggH Gene of Escherichia coli Encodes a tRNA (m7G46) Methyltransferase
Roovers, Martine, Oudjama, Yamina, Wattiez, Ruddy, Tricot, Catherine, Stalon, Victor, ...
We cloned, expressed, and purified the Escherichia coli YggH protein and show that it catalyzes the S-adenosyl-l-methionine-dependent formation of N7-methylguanosine at position 46 (m7G46) in tRNA....
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
Ginalski, Krzysztof, Pas, Jakub, Wyrwicz, Lucjan S., Grotthuss, Marcin Von, Bujnicki, Janusz M., Rychlewski, Leszek
ORFeus is a fully automated, sensitive protein sequence similarity search server available to the academic community via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/). The goal of...
GeneSilico protein structure prediction meta-server
Kurowski, Michal A., Bujnicki, Janusz M.
Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It...
Sequence–structure–function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase
Mouaikel, John, Bujnicki, Janusz M., Tazi, Jamal, Bordonné, Rémy
The Saccharomyces cerevisiae Tgs1 methyltransferase (MTase) is responsible for conversion of the m7G caps of snRNAs and snoRNAs to a 2,2,7- trimethylguanosine structure. To learn more about the...
Maravić, Gordana, Bujnicki, Janusz M., Feder, Marcin, Pongor, Sándor, Flögel, Mirna
The Erm family of adenine-N6 methyltransferases (MTases) is responsible for the development of resistance to macrolide–lincosamide–streptogramin B antibiotics through the methylation of 23S...
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB
Kurowski, Michal A, Bhagwat, Ashok S, Papaj, Grzegorz, Bujnicki, Janusz M
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
Roovers, Martine, Wouters, Johan, Bujnicki, Janusz M., Tricot, Catherine, Stalon, Victor, Grosjean, Henri, ...
The modified nucleoside 1-methyladenosine (m1A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic...
Bujnicki, Janusz M., Feder, Marcin, Ayres, Chastity L., Redman, Kent L.
Three types of methyltransferases (MTases) generate 5-methylpyrimidine in nucleic acids, forming m5U in RNA, m5C in RNA and m5C in DNA. The DNA:m5C MTases have been extensively studied by...
COLORADO3D, a web server for the visual analysis of protein structures
Sasin, Joanna M., Bujnicki, Janusz M.
COLORADO3D is a World Wide Web server for the visual presentation of three-dimensional (3D) protein structures. COLORADO3D indicates the presence of potential errors (detected by ANOLEA, PROSAII,...
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily
Saravanan, Matheshwaran, Bujnicki, Janusz M., Cymerman, Iwona A., Rao, Desirazu N., Nagaraja, Valakunja
The restriction endonuclease (REase) R.KpnI is an orthodox Type IIP enzyme, which binds to DNA in the absence of metal ions and cleaves the DNA sequence 5′-GGTAC^C-3′ in the presence of Mg2+ as...
A homology model of restriction endonuclease SfiI in complex with DNA
Chmiel, Agnieszka A, Bujnicki, Janusz M, Skowronek, Krzysztof J
Pawlak, Sebastian D., Radlinska, Monika, Chmiel, Agnieszka A., Bujnicki, Janusz M., Skowronek, Krzysztof J.
Thus far, identification of functionally important residues in Type II restriction endonucleases (REases) has been difficult using conventional methods. Even though known REase structures share a...
Purushothaman, Suresh K., Bujnicki, Janusz M., Grosjean, Henri, Lapeyre, Bruno
N2-Monomethylguanosine-10 (m2G10) and N2,N2-dimethylguanosine-26 (m22G26) are the only two guanosine modifications that have been detected in tRNA from nearly all archaea and eukaryotes but not in...
Ishikawa, Ken, Watanabe, Miki, Kuroita, Toshihiro, Uchiyama, Ikuo, Bujnicki, Janusz M., Kawakami, Bunsei, ...
To search for restriction endonucleases, we used a novel plant-based cell-free translation procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the related genomes of...
MODOMICS: a database of RNA modification pathways
Dunin-Horkawicz, Stanislaw, Czerwoniec, Anna, Gajda, Michal J., Feder, Marcin, Grosjean, Henri, Bujnicki, Janusz M.
MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in...
BUJNICKI, JANUSZ M., OUDJAMA, YAMINA, ROOVERS, MARTINE, OWCZAREK, SYLWIA, CAILLET, JOËL, DROOGMANS, LOUIS
The gene encoding the bifunctional enzyme MnmC that catalyzes the two last steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2U) in tRNA has been previously mapped at about 50 min...
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase
Zegers, Ingrid, Gigot, Daniel, Van Vliet, Françoise, Tricot, Catherine, Aymerich, Stéphane, Bujnicki, Janusz M., ...
The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 Å. This is the first structure of a member of the TrmB family to be...
Obarska, Agnieszka, Blundell, Alex, Feder, Marcin, Vejsadová, Štěpánka, Šišáková, Eva, Weiserová, Marie, ...
Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restriction–modification (R-M) enzymes MjaXIP and MgeORF438 have...
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain
Gabant, Guillaume, Auxilien, Sylvie, Tuszynska, Irina, Locard, Marie, Gajda, Michal J., Chaussinand, Guylaine, ...
The tRNA:m22G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine...
Phylogenomic analysis of the GIY-YIG nuclease superfamily
Dunin-Horkawicz, Stanislaw, Feder, Marcin, Bujnicki, Janusz M
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase
Purta, Elzbieta, Van Vliet, Françoise, Tkaczuk, Karolina L, Dunin-Horkawicz, Stanislaw, Mori, Hirotada, Droogmans, Louis, ...
Complete Cap 4 Formation Is Not Required for Viability in Trypanosoma brucei†
Zamudio, Jesse R., Mittra, Bidyottam, Zeiner, Gusti M., Feder, Marcin, Bujnicki, Janusz M., Sturm, Nancy R., ...
In kinetoplastids spliced leader (SL) RNA is trans-spliced onto the 5′ ends of all nuclear mRNAs, providing a universal exon with a unique cap. Mature SL contains an m7G cap, ribose 2′-O...
Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop
Pintard, Lionel, Lecointe, François, Bujnicki, Janusz M., Bonnerot, Claire, Grosjean, Henri, Lapeyre, Bruno
The genome of Saccharomyces cerevisiae encodes three close homologues of the Escherichia coli 2′-O-rRNA methyltransferase FtsJ/RrmJ, designated Trm7p, Spb1p and Mrm2p. We present evidence that...
MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase
Pintard, Lionel, Bujnicki, Janusz M., Lapeyre, Bruno, Bonnerot, Claire
Mitochondria of the yeast Saccharomyces cerevisiae assemble their ribosomes from ribosomal proteins, encoded by the nuclear genome (with one exception), and rRNAs of 15S and 21S, encoded by the...
Droogmans, Louis, Roovers, Martine, Bujnicki, Janusz M., Tricot, Catherine, Hartsch, Thomas, Stalon, Victor, ...
N1-methyladenosine (m1A) is found at position 58 in the T-loop of many tRNAs. In yeast, the formation of this modified nucleoside is catalyzed by the essential tRNA (m1A58) methyltransferase, a...
The yggH Gene of Escherichia coli Encodes a tRNA (m7G46) Methyltransferase
Roovers, Martine, Oudjama, Yamina, Wattiez, Ruddy, Tricot, Catherine, Stalon, Victor, ...
We cloned, expressed, and purified the Escherichia coli YggH protein and show that it catalyzes the S-adenosyl-l-methionine-dependent formation of N7-methylguanosine at position 46 (m7G46) in tRNA....
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
Ginalski, Krzysztof, Pas, Jakub, Wyrwicz, Lucjan S., Grotthuss, Marcin Von, Bujnicki, Janusz M., Rychlewski, Leszek
ORFeus is a fully automated, sensitive protein sequence similarity search server available to the academic community via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/). The goal of...
GeneSilico protein structure prediction meta-server
Kurowski, Michal A., Bujnicki, Janusz M.
Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It...
Sequence–structure–function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase
Mouaikel, John, Bujnicki, Janusz M., Tazi, Jamal, Bordonné, Rémy
The Saccharomyces cerevisiae Tgs1 methyltransferase (MTase) is responsible for conversion of the m7G caps of snRNAs and snoRNAs to a 2,2,7- trimethylguanosine structure. To learn more about the...
Maravić, Gordana, Bujnicki, Janusz M., Feder, Marcin, Pongor, Sándor, Flögel, Mirna
The Erm family of adenine-N6 methyltransferases (MTases) is responsible for the development of resistance to macrolide–lincosamide–streptogramin B antibiotics through the methylation of 23S...