Genomes and Genes
Experts and Doctors on escherichia coli proteins in Warsaw, Masovian Voivodeship, Poland
Locale: Warsaw, Masovian Voivodeship, Poland
Topic: escherichia coli proteins
- Bujnicki J, Rychlewski L. RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics. 2002;3:10 pubmed..The results provide novel insight into the mechanism of m2G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases. ..
- Bykowski T, van der Ploeg J, Iwanicka Nowicka R, Hryniewicz M. The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess. Mol Microbiol. 2002;43:1347-58 pubmed..Our data comprise the first evidence that APS may act as the negative cofactor of the transcriptional regulator Cbl, and that APS, and not sulphate itself, serves as the signalling molecule for sulphate excess. ..
- Bujnicki J, Rychlewski L. Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs. Acta Microbiol Pol. 2000;49:253-60 pubmed..The N-terminal region of YgdE, which has no counterpart in RrmJ, is predicted to form an independent domain, possibly involved in target recognition. ..
- Maciejewska A, Poznanski J, Kaczmarska Z, Krowisz B, Nieminuszczy J, Polkowska Nowakowska A, et al. AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. J Biol Chem. 2013;288:432-41 pubmed publisher..Molecular modeling of these adducts bound by AlkB allowed evaluation of the participation of their possible conformational states in the enzymatic reaction...
- Janion C, Sikora A, Nowosielska A, Grzesiuk E. E. coli BW535, a triple mutant for the DNA repair genes xth, nth, and nfo, chronically induces the SOS response. Environ Mol Mutagen. 2003;41:237-42 pubmed..MutT and MutY proteins, when active, protect bacteria from mutations induced by 8-oxoG lesions in DNA. This suggests that accumulation of abasic sites, but not 8-oxoG residues in DNA, induce the SOS response. ..
- Adamczyk Popławska M, Kondrzycka A, Urbanek K, Piekarowicz A. Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems. Microbiology. 2003;149:3311-9 pubmed..The authors propose that the type IC family of R-M systems could consist of several complementation subgroups whose specificity would depend on differences in the conserved regions of the HsdS polypeptide. ..
- Purta E, van Vliet F, Tkaczuk K, Dunin Horkawicz S, Mori H, Droogmans L, et al. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol. 2006;7:23 pubmed
- Ginalski K. Comparative modeling for protein structure prediction. Curr Opin Struct Biol. 2006;16:172-7 pubmed..For difficult targets, for which the most significant progress in recent years has been observed, optimal template selection and alignment accuracy are still the major problems. ..
- Purta E, van Vliet F, Tricot C, De Bie L, Feder M, Skowronek K, et al. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins. 2005;59:482-8 pubmed
- Banach Orlowska M, Fijalkowska I, Schaaper R, Jonczyk P. DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol Microbiol. 2005;58:61-70 pubmed..A second role of Pol II is to protect mismatched 3' termini against the mutagenic action of polymerase IV (dinB product). Overall, Pol II may be considered a main player in the polymerase trafficking at the replication fork. ..
- Prokopowicz M, Greń B, Cieśla J, Kierdaszuk B. Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A. Biophys Chem. 2017;230:99-108 pubmed publisher..Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems. ..
- Kalwarczyk T, Tabaka M, Holyst R. Biologistics--diffusion coefficients for complete proteome of Escherichia coli. Bioinformatics. 2012;28:2971-8 pubmed publisher..Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. email@example.com. Supplementary data are available at Bioinformatics Online. ..
- Maciejewska A, Sokołowska B, Nowicki A, Kuśmierek J. The role of AlkB protein in repair of 1,N?-ethenoadenine in Escherichia coli cells. Mutagenesis. 2011;26:401-6 pubmed publisher..coli cells. The observed differences of mutation frequencies in the various mutant strains assayed indicate that Mug glycosylase is also engaged in the repair of ?A, whereas the role the AlkA glycosylase in this repair is negligible. ..
- Kuban W, Banach Orlowska M, Schaaper R, Jonczyk P, Fijalkowska I. Role of DNA polymerase IV in Escherichia coli SOS mutator activity. J Bacteriol. 2006;188:7977-80 pubmed..Here we show that a significant fraction of this effect also requires DNA polymerase IV (dinB gene product). ..
- Grudniak A, Nowicka Sans B, Maciag M, Wolska K. Influence of Escherichia coli DnaK and DnaJ molecular chaperones on tryptophanase (TnaA) amount and GreA, GreB stability. Folia Microbiol (Praha). 2004;49:507-12 pubmed..The half-life of GreA and GreB proteins (being activators of transcription elongation of the tna operon) are diminished in both mutants suggesting the involvement of DnaK and DnaJ in the stability of these proteins. ..
- Marcyjaniak M, Odintsov S, Sabala I, Bochtler M. Peptidoglycan amidase MepA is a LAS metallopeptidase. J Biol Chem. 2004;279:43982-9 pubmed..We conclude that MepA-type peptidases are LAS enzymes. ..
- Karpinski P, Grudniak A, Wolska K. Effect of mutations in dnaK and dnaJ genes on cysteine operon expression in Escherichia coli. Folia Microbiol (Praha). 2002;47:371-4 pubmed
- Zaim J, Kierzek A. The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer. Nucleic Acids Res. 2003;31:1444-54 pubmed..A comparison of the LTTR DBD model with the structures of other HTH proteins also provides insights into the interaction of LTTRs with the C-terminal domain of the RNA polymerase alpha subunit. ..
- Bujnicki J, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA. 2004;10:1236-42 pubmed..We have cloned, expressed, and purified the YfcK protein and demonstrated that it catalyzes the formation of mnm5s2U in tRNA. Thus, we suggest to rename YfcK as MnmC. ..
- Firczuk M, Bochtler M. Mutational analysis of peptidoglycan amidase MepA. Biochemistry. 2007;46:120-8 pubmed..Mutation of residue W203 to aspartate impairs substrate binding. ..
- Kosinski J, Plotz G, Guarné A, Bujnicki J, Friedhoff P. The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol. 2008;382:610-27 pubmed publisher..Finally, we demonstrate that the conserved residues of the metal ion binding domain are crucial for MMR activity of MutLalpha in vitro. ..
- Bujnicki J. Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. FASEB J. 2000;14:2365-8 pubmed
- Janowska B, Komisarski M, Prorok P, Sokołowska B, Kuśmierek J, Janion C, et al. Nucleotide excision repair and recombination are engaged in repair of trans-4-hydroxy-2-nonenal adducts to DNA bases in Escherichia coli. Int J Biol Sci. 2009;5:611-20 pubmed..These transitions could have resulted from high reactivity of HNE with G and C, and induction of SOS-independent mutations. ..
- Tudek B, van Zeeland A, Kusmierek J, Laval J. Activity of Escherichia coli DNA-glycosylases on DNA damaged by methylating and ethylating agents and influence of 3-substituted adenine derivatives. Mutat Res. 1998;407:169-76 pubmed..Taken together, these results suggest that hydrophobic interactions are involved in the mechanism of inhibition and/or recognition and excision of alkylated purines by TagA protein. ..
- Nowosielska A, Janion C, Grzesiuk E. Effect of deletion of SOS-induced polymerases, pol II, IV, and V, on spontaneous mutagenesis in Escherichia coli mutD5. Environ Mol Mutagen. 2004;43:226-34 pubmed..We postulate that the proofreading activity of pol II excises DNA lesions in exponentially growing cells, whereas pol V and pol IV are more active in stationary-phase cultures. ..
- Koprowski P, Kubalski A. C termini of the Escherichia coli mechanosensitive ion channel (MscS) move apart upon the channel opening. J Biol Chem. 2003;278:11237-45 pubmed..We propose that the as yet undefined C-terminal region may form a cytoplasmic gate of the channel. The results are discussed and interpreted based on the recently released quaternary structure of the channel. ..
- Olejnik K, Kraszewska E. Cloning and characterization of an Arabidopsis thaliana Nudix hydrolase homologous to the mammalian GFG protein. Biochim Biophys Acta. 2005;1752:133-41 pubmed..2 mM and 2.7 s(-1) respectively. The products of ADP-ribose hydrolysis were AMP and ribose-5-phosphate. The optimal activity was at alkaline pH (8.5) with Mg2+ (5 mM) ions as the cofactor. The protein exists as a dimmer in solution. ..