Catalytic, Computational, and Evolutionary Analysis of the d-Lactate Dehydrogenases Responsible for d-Lactic Acid Production in Lactic Acid Bacteria

Journal of Agricultural and Food Chemistry
Baolei JiaChe Ok Jeon

Abstract

d-Lactate dehydrogenase (d-LDH) catalyzes the reversible reaction pyruvate + NADH + H+ ↔ lactate + NAD+, which is a principal step in the production of d-lactate in lactic acid bacteria. In this study, we identified and characterized the major d-LDH (d-LDH1) from three d-LDHs in Leuconostoc mesenteroides, which has been extensively used in food processing. A molecular simulation study of d-LDH1 showed that the conformation changes during substrate binding. During catalysis, Tyr101 and Arg235 bind the substrates by hydrogen bonds and His296 acts as a general acid/base for proton transfer. These residues are also highly conserved and have coevolved. Point mutations proved that the substrate binding sites and catalytic site are crucial for enzyme activity. Network and phylogenetic analyses indicated that d-LDH1 and the homologues are widely distributed but are most abundant in bacteria and fungi. This study expands the understanding of the functions, catalytic mechanism, and evolution of d-LDH.

References

Mar 1, 1980·Microbiological Reviews·E I Garvie
Feb 24, 1999·Critical Reviews in Food Science and Nutrition·A S NaiduR A Clemens
Mar 11, 2000·European Journal of Biochemistry·S KochharJ E Germond
Jun 14, 2000·Current Opinion in Microbiology·W N KoningsB Poolman
Feb 15, 2001·Current Microbiology·S AvalloneJ P Guiraud
Jun 11, 2002·Journal of Molecular Biology·Adelia RazetoVictor S Lamzin
Dec 27, 2002·The Journal of General and Applied Microbiology·Akira ManomeKazuo Komagata
Jun 28, 2005·Nucleic Acids Research·John C GordonAlexey Onufriev
Mar 30, 2006·Journal of Bioscience and Bioengineering·Nobuhiro IshidaHaruo Takahashi
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Dec 23, 2011·International Journal of Food Microbiology·Ji Young JungChe Ok Jeon
May 30, 2013·Nucleic Acids Research·Franco L SimonettiCristina Marino Buslje
Jun 12, 2013·Current Protocols in Bioinformatics·William R Pearson
May 6, 2014·International Journal of Biological Macromolecules·Sangwoo KimKyung-Jin Kim
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium
Apr 4, 2015·Expert Opinion on Drug Discovery·Samuel Genheden, Ulf Ryde
Jul 8, 2015·Applied and Environmental Microbiology·Lingfeng ZhuYanhe Ma
Aug 20, 2015·Critical Reviews in Biotechnology·Veeresh Juturu, Jin Chuan Wu
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Dec 7, 2016·Biochimica Et Biophysica Acta. General Subjects·Baolei JiaChe Ok Jeon
Aug 30, 2017·Biochimica Et Biophysica Acta. General Subjects·Baolei JiaChe Ok Jeon
Jan 13, 2018·Frontiers in Plant Science·Baolei JiaYuan Hu Xuan
Feb 3, 2018·Chembiochem : a European Journal of Chemical Biology·Divya Singh, Srabanti Chaudhury

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Citations

Oct 30, 2019·Journal of Molecular Evolution·Antoine Danchin, Pablo Iván Nikel
Aug 5, 2020·Applied Microbiology and Biotechnology·Se Hee LeeChe Ok Jeon
Mar 20, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Baolei JiaChe Ok Jeon
Jul 16, 2020·Applied Microbiology and Biotechnology·Juliana BleckwedelRaúl Ricardo Raya
Apr 22, 2021·Scientific Data·Tae Woong WhonSeong Woon Roh
Aug 21, 2021·Critical Reviews in Biotechnology·Ernesta AugustinieneNaglis Malys

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