Krzysztof Kuchta

Publications (3)21.41 Total impact

• Source

  Available from: PubMed Central

  Article: DNAtraffic--a new database for systems biology of DNA dynamics during the cell life.

  Krzysztof Kuchta, Daniela Barszcz, Elzbieta Grzesiuk, Pawel Pomorski, Joanna Krwawicz
  [show abstract] [hide abstract]
  ABSTRACT: DNAtraffic (http://dnatraffic.ibb.waw.pl/) is dedicated to be a unique comprehensive and richly annotated database of genome dynamics during the cell life. It contains extensive data on the nomenclature, ontology, structure and function of proteins related to the DNA integrity mechanisms such as chromatin remodeling, histone modifications, DNA repair and damage response from eight organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on the diseases related to the assembled human proteins. DNAtraffic is richly annotated in the systemic information on the nomenclature, chemistry and structure of DNA damage and their sources, including environmental agents or commonly used drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA network analysis. Database includes illustrations of pathways, damage, proteins and drugs. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines, it has to be extensively linked to numerous external data sources. Our database represents the result of the manual annotation work aimed at making the DNAtraffic much more useful for a wide range of systems biology applications.
  Nucleic Acids Research 11/2011; 40(Database issue):D1235-40. · 8.03 Impact Factor
• Source

  Available from: PubMed Central

  Article: Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human.

  Krzysztof Kuchta, Lukasz Knizewski, Lucjan S Wyrwicz, Leszek Rychlewski, Krzysztof Ginalski
  [show abstract] [hide abstract]
  ABSTRACT: This article presents a comprehensive review of large and highly diverse superfamily of nucleotidyltransferase fold proteins by providing a global picture about their evolutionary history, sequence-structure diversity and fulfilled functional roles. Using top-of-the-line homology detection method combined with transitive searches and fold recognition, we revised the realm of these superfamily in numerous databases of catalogued protein families and structures, and identified 10 new families of nucleotidyltransferase fold. These families include hundreds of previously uncharacterized and various poorly annotated proteins such as Fukutin/LICD, NFAT, FAM46, Mab-21 and NRAP. Some of these proteins seem to play novel important roles, not observed before for this superfamily, such as regulation of gene expression or choline incorporation into cell membrane. Importantly, within newly detected families we identified 25 novel superfamily members in human genome. Among these newly assigned members are proteins known to be involved in congenital muscular dystrophy, neurological diseases and retinal pigmentosa what sheds some new light on the molecular background of these genetic disorders. Twelve of new human nucleotidyltransferase fold proteins belong to Mab-21 family known to be involved in organogenesis and development. The determination of specific biological functions of these newly detected proteins remains a challenging task.
  Nucleic Acids Research 10/2009; 37(22):7701-14. · 8.03 Impact Factor
• Article: Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.

  Lukasz Knizewski, Kamil Steczkiewicz, Krzysztof Kuchta, Lucjan Wyrwicz, Dariusz Plewczynski, Andrzej Kolinski, Leszek Rychlewski, Krzysztof Ginalski
  Cell cycle (Georgetown, Tex.) 03/2008; 7(4):542-4. · 5.36 Impact Factor