Prediction of coenzyme specificity in dehydrogenases/reductases. A hidden Markov model-based method and its application on complete genomes

The FEBS Journal
Yvonne Kallberg, B Persson

Abstract

Dehydrogenases and reductases are enzymes of fundamental metabolic importance that often adopt a specific structure known as the Rossmann fold. This fold, consisting of a six-stranded beta-sheet surrounded by alpha-helices, is responsible for coenzyme binding. We have developed a method to identify Rossmann folds and predict their coenzyme specificity (NAD, NADP or FAD) using only the amino acid sequence as input. The method is based upon hidden Markov models and sequence pattern analysis. The prediction sensitivity is 79% and the selectivity close to 100%. The method was applied on a set of 68 genomes, representing the three kingdoms archaea, bacteria and eukaryota. In prokaryotes, 3% of the genes were found to code for Rossmann-fold proteins, while the corresponding ratio in eukaryotes is only around 1%. In all genomes, NAD is the most preferred cofactor (41-49%), followed by NADP with 30-38%, while FAD is the least preferred cofactor (21%). However, the NAD preponderance over NADP is most pronounced in archaea, and least in eukaryotes. In all three kingdoms, only 3-8% of the Rossmann proteins are predicted to have more than one membrane-spanning segment, which is much lower than the frequency of membrane proteins in general....Continue Reading

References

May 11, 1978·Nature·G E SchulzE F Pai
Jan 1, 1996·Methods in Enzymology·S E BrennerA G Murzin
Jan 27, 1999·Bioinformatics·S R Eddy
Dec 28, 1999·FEBS Letters·J B JacksonS A White
Sep 22, 2001·Protein Science : a Publication of the Protein Society·J Liu, B Rost
Sep 17, 2002·European Journal of Biochemistry·Yvonne KallbergBengt Persson
Dec 19, 2003·Nucleic Acids Research·John-Marc ChandoniaSteven E Brenner
Jan 6, 2004·Nucleic Acids Research·Martin C FrithZhiping Weng
Apr 28, 2004·Journal of Molecular Biology·Lukas KällErik L L Sonnhammer
Dec 21, 2004·Nucleic Acids Research·Nicola J MulderCathy H Wu
Dec 21, 2004·Nucleic Acids Research·T HubbardE Birney

❮ Previous
Next ❯

Citations

Nov 9, 2007·Applied Microbiology and Biotechnology·Matthias Hess, Garabed Antranikian
Jul 5, 2008·Plant Physiology·Hyong Woo ChoiByung Kook Hwang
Aug 18, 2012·BMC Evolutionary Biology·Agustín Sola-CarvajalÁlvaro Sánchez-Ferrer
Aug 6, 2011·PloS One·Rosa TarríoFrancisco Rodríguez-Trelles
Dec 6, 2008·Molecular Biotechnology·Erika Nahomy Marino-MarmolejoLeticia Santos
Nov 26, 2008·Chemico-biological Interactions·Bengt PerssonUdo Oppermann
Jan 29, 2008·The Plant Journal : for Cell and Molecular Biology·Andrea BrockBirgit Dräger
Dec 15, 2012·Archives of Insect Biochemistry and Physiology·Jaime G MayoralAdrian G Turjanski
Nov 2, 2011·Biochemical and Biophysical Research Communications·Xu LiuDongzhi Wei
Jun 11, 2016·Journal of Photochemistry and Photobiology. B, Biology·Binuraj R K MenonDerren J Heyes
Sep 17, 2017·The Journal of Cell Biology·Vivien KrügerChris Meisinger
Feb 14, 2014·Proteins·Henrik Marcus Geertz-HansenThomas Nordahl Petersen
Feb 1, 2019·Critical Reviews in Biotechnology·Jianhong AnYan Xu
May 15, 2007·FEMS Yeast Research·Tiziana LodiPhilippe V Baret
Mar 8, 2017·Applied Microbiology and Biotechnology·Han-Yu WangMeng -Gen Ma
May 23, 2018·Proceedings of the National Academy of Sciences of the United States of America·Alysha K LeePaula V Welander
Aug 25, 2011·The Plant Cell·Francis X Cunningham, Elisabeth Gantt

❮ Previous
Next ❯

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.