General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH

Brinkmann-Chen, Sabine; Flock, Tilman; Cahn, Jackson K. B.; Snow, Christopher D.; Brustad, Eric M.; McIntosh, John A.; Meinhold, Peter; Zhang, Liang; Arnold, Frances H.

doi:10.1073/pnas.1306073110

General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH

Journal Article · Mon Jun 17 00:00:00 EDT 2013 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1306073110· OSTI ID:1128893

Brinkmann-Chen, Sabine ^[1]; Flock, Tilman ^[2]; Cahn, Jackson K. B. ^[1]; Snow, Christopher D. ^[3]; Brustad, Eric M. ^[4]; McIntosh, John A. ^[1]; Meinhold, Peter ^[5]; Zhang, Liang ^[1]; Arnold, Frances H. ^[1]

California Inst. of Technology (CalTech), Pasadena, CA (United States)
California Inst. of Technology (CalTech), Pasadena, CA (United States); MRC Lab. of Molecular Biology, Cambridge (United Kingdom)
California Inst. of Technology (CalTech), Pasadena, CA (United States); Colorado State Univ., Fort Collins, CO (United States)
California Inst. of Technology (CalTech), Pasadena, CA (United States); Univ. of North Carolina, Chapel Hill, NC (United States)
Gevo, Inc., Englewood, CO (United States)

To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymes having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. As a result, high-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1128893

Report Number(s):: SLAC-REPRINT--2014-040

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 27 Vol. 110; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

References (38)

Computational design of Candida boidinii xylose reductase for altered cofactor specificity Khoury, George A.; Fazelinia, Hossein; Chin, Jonathan W. Protein Science, Vol. 18, Issue 10 https://doi.org/10.1002/pro.227	journal	October 2009
Reversal of the Nucleotide Specificity of Ketol Acid Reductoisomerase by Site-Directed Mutagenesis Identifies the NADPH Binding Site1 Rane, Madhavi J.; Calvo, K. C. Archives of Biochemistry and Biophysics, Vol. 338, Issue 1 https://doi.org/10.1006/abbi.1996.9802	journal	February 1997
Engineering of Pyridine Nucleotide Specificity of Nitrate Reductase: Mutagenesis of Recombinant CytochromebReductase Fragment ofNeurospora crassaNADPH:Nitrate Reductase Shiraishi, Naomasa; Croy, Cynthia; Kaur, John Archives of Biochemistry and Biophysics, Vol. 358, Issue 1 https://doi.org/10.1006/abbi.1998.0827	journal	October 1998
Fermentative production of branched chain amino acids: a focus on metabolic engineering Park, Jin Hwan; Lee, Sang Yup Applied Microbiology and Biotechnology, Vol. 85, Issue 3 https://doi.org/10.1007/s00253-009-2307-y	journal	October 2009
[19] Rapid and efficient site-specific mutagenesis without phenotypic selection Kunkel, Thomas A.; Roberts, John D.; Zakour, Richard A. Methods in Enzymology, p. 367-382 https://doi.org/10.1016/0076-6879(87)54085-X	book	January 1987
Purification and Properties of the Acetohydroxy Acid Isomeroreductase of Salmonella typhimurium Arfin, S. M.; Umbarger, H. E. Journal of Biological Chemistry, Vol. 244, Issue 5 https://doi.org/10.1016/S0021-9258(18)91816-8	journal	March 1969
Crystal Structure of Class I Acetohydroxy Acid Isomeroreductase from Pseudomonas aeruginosa Ahn, Hyung Jun; Eom, Su Jung; Yoon, Hye-Jin Journal of Molecular Biology, Vol. 328, Issue 2, p. 505-515 https://doi.org/10.1016/S0022-2836(03)00264-X	journal	April 2003
Rational design of novel mutants of fungal 17β-hydroxysteroid dehydrogenase Kristan, Katja; Stojan, Jure; Adamski, Jerzy Journal of Biotechnology, Vol. 129, Issue 1 https://doi.org/10.1016/j.jbiotec.2006.11.025	journal	March 2007
Conformational Changes in a Plant Ketol-Acid Reductoisomerase upon Mg2+ and NADPH Binding as Revealed by Two Crystal Structures Leung, Eleanor W. W.; Guddat, Luke W. Journal of Molecular Biology, Vol. 389, Issue 1 https://doi.org/10.1016/j.jmb.2009.04.012	journal	May 2009
Bacterial and Plant Ketol-Acid Reductoisomerases Have Different Mechanisms of Induced Fit during the Catalytic Cycle Wong, Sze-Ho; Lonhienne, Thierry G. A.; Winzor, Donald J. Journal of Molecular Biology, Vol. 424, Issue 3-4 https://doi.org/10.1016/j.jmb.2012.09.018	journal	December 2012
Metabolic engineering of Escherichia coli for 1-butanol production Atsumi, Shota; Cann, Anthony F.; Connor, Michael R. Metabolic Engineering, Vol. 10, Issue 6, p. 305-311 https://doi.org/10.1016/j.ymben.2007.08.003	journal	November 2008
Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli Bastian, Sabine; Liu, Xiang; Meyerowitz, Joseph T. Metabolic Engineering, Vol. 13, Issue 3, p. 345-352 https://doi.org/10.1016/j.ymben.2011.02.004	journal	May 2011
Enzymology, Structure, and Dynamics of Acetohydroxy Acid Isomeroreductase Dumas, Renaud; Biou, Valérie; Halgand, Frédéric Accounts of Chemical Research, Vol. 34, Issue 5 https://doi.org/10.1021/ar000082w	journal	May 2001
Interaction of pyrophosphate moieties with .alpha.-helixes in dinucleotide-binding proteins Wierenga, Rik K.; De Maeyer, Marc C. H.; Hol, Wim G. J. Biochemistry, Vol. 24, Issue 6 https://doi.org/10.1021/bi00327a012	journal	March 1985
Oxalyl hydroxamates as reaction-intermediate analogs for ketol-acid reductoisomerase Aulabaugh, Ann; Schloss, John V. Biochemistry, Vol. 29, Issue 11 https://doi.org/10.1021/bi00463a027	journal	March 1990
Chemical and biological evolution of a nucleotide-binding protein Rossmann, Michael G.; Moras, Dino; Olsen, Kenneth W. Nature, Vol. 250, Issue 5463 https://doi.org/10.1038/250194a0	journal	July 1974
Redesign of the coenzyme specificity of a dehydrogenase by protein engineering Scrutton, Nigel S.; Berry, Alan; Perham, Richard N. Nature, Vol. 343, Issue 6253 https://doi.org/10.1038/343038a0	journal	January 1990
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels Atsumi, Shota; Hanai, Taizo; Liao, James C. Nature, Vol. 451, Issue 7174, p. 86-89 https://doi.org/10.1038/nature06450	journal	January 2008
The coenzyme specificity of Candida tenuis xylose reductase (AKR2B5) explored by site-directed mutagenesis and X-ray crystallography Petschacher, Barbara; Leitgeb, Stefan; Kavanagh, Kathryn L. Biochemical Journal, Vol. 385, Issue 1 https://doi.org/10.1042/BJ20040363	journal	December 2004
Branched-chain-amino-acid biosynthesis in plants: molecular cloning and characterization of the gene encoding acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase) from Arabidopsis thaliana (thale cress) Dumas, R.; Curien, G.; DeRose, R. T. Biochemical Journal, Vol. 294, Issue 3 https://doi.org/10.1042/bj2940821	journal	September 1993
Protein stability promotes evolvability Bloom, J. D.; Labthavikul, S. T.; Otey, C. R. Proceedings of the National Academy of Sciences, Vol. 103, Issue 15, p. 5869-5874 https://doi.org/10.1073/pnas.0510098103	journal	March 2006
Cation-pi interactions in structural biology Gallivan, J. P.; Dougherty, D. A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 17 https://doi.org/10.1073/pnas.96.17.9459	journal	August 1999
Modification of the Nucleotide Cofactor-binding Site of Cytochrome P-450 Reductase to Enhance Turnover with NADH in Vivo Elmore, C. Lee; Porter, Todd D. Journal of Biological Chemistry, Vol. 277, Issue 50 https://doi.org/10.1074/jbc.M210173200	journal	October 2002
Complete Reversal of Coenzyme Specificity by Concerted Mutation of Three Consecutive Residues in Alcohol Dehydrogenase Rosell, Albert; Valencia, Eva; Ochoa, Wendy F. Journal of Biological Chemistry, Vol. 278, Issue 42 https://doi.org/10.1074/jbc.M307384200	journal	August 2003
The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65Aresolution Biou, V. The EMBO Journal, Vol. 16, Issue 12 https://doi.org/10.1093/emboj/16.12.3405	journal	June 1997
Sequence logos: a new way to display consensus sequences Schneider, Thomas D.; Stephens, R. Michael Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6097	journal	January 1990
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Boeckmann, B. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg095	journal	January 2003
A new bioinformatics analysis tools framework at EMBL-EBI Goujon, M.; McWilliam, H.; Li, W. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq313	journal	May 2010
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Structure of spinach acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxymethylvalerate, manganese and (phospho)-ADP-ribose Thomazeau, Karine; Dumas, Renaud; Halgand, Frédéric Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 4 https://doi.org/10.1107/S0907444900001694	journal	April 2000
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Scaling and assessment of data quality Evans, Philip Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82 https://doi.org/10.1107/S0907444905036693	journal	December 2005
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
The crystal structure of a bacterial Class II ketol-acid reductoisomerase: Domain conservation and evolution Tyagi, Rajiv; Duquerroy, Stephane; Navaza, Jorge Protein Science, Vol. 14, Issue 12 https://doi.org/10.1110/ps.051791305	journal	December 2005
Improvement of the Redox Balance Increases l-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions Hasegawa, Satoshi; Uematsu, Kimio; Natsuma, Yumi Applied and Environmental Microbiology, Vol. 78, Issue 3 https://doi.org/10.1128/AEM.07056-11	journal	December 2011
Characterization of enzymes of the branched-chain amino acid biosynthetic pathway in Methanococcus spp. Xing, R. Y.; Whitman, W. B. Journal of Bacteriology, Vol. 173, Issue 6 https://doi.org/10.1128/jb.173.6.2086-2092.1991	journal	January 1991
Altering the coenzyme preference of xylose reductase to favor utilization of NADH enhances ethanol yield from xylose in a metabolically engineered strain of Saccharomyces cerevisiae Petschacher, Barbara; Nidetzky, Bernd Microbial Cell Factories, Vol. 7, Issue 1 https://doi.org/10.1186/1475-2859-7-9	journal	January 2008

Cited By (19)

Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology You, Chun; Huang, Rui; Wei, Xinlei Synthetic and Systems Biotechnology, Vol. 2, Issue 3 https://doi.org/10.1016/j.synbio.2017.09.002	journal	September 2017
NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius Chen, Chin-Yu; Ko, Tzu-Ping; Lin, Kuan-Fu Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-25361-4	journal	May 2018
Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity Maddock, Danielle J.; Patrick, Wayne M.; Gerth, Monica L. Protein Engineering Design and Selection, Vol. 28, Issue 8 https://doi.org/10.1093/protein/gzv028	journal	June 2015
An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors Laurino, Paola; Tóth-Petróczy, Ágnes; Meana-Pañeda, Rubén PLOS Biology, Vol. 14, Issue 3 https://doi.org/10.1371/journal.pbio.1002396	journal	March 2016
Protein Engineering for Nicotinamide Coenzyme Specificity in Oxidoreductases: Attempts and Challenges Chánique, Andrea M.; Parra, Loreto P. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00194	journal	February 2018
Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen Lemaire, Olivier Nicolas; Müller, Marie-Caroline; Kahnt, Jörg Biomolecules, Vol. 11, Issue 11 https://doi.org/10.3390/biom11111679	journal	November 2021
A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation Murciano-Calles, Javier; Romney, David K.; Brinkmann-Chen, Sabine Angewandte Chemie, Vol. 128, Issue 38 https://doi.org/10.1002/ange.201606242	journal	August 2016
Regulating Cofactor Balance In Vivo with a Synthetic Flavin Analogue Tan, Zhuotao; Zhu, Chenjie; Fu, Jingwen Angewandte Chemie, Vol. 130, Issue 50 https://doi.org/10.1002/ange.201810881	journal	November 2018
A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation Murciano-Calles, Javier; Romney, David K.; Brinkmann-Chen, Sabine Angewandte Chemie International Edition, Vol. 55, Issue 38 https://doi.org/10.1002/anie.201606242	journal	August 2016
Regulating Cofactor Balance In Vivo with a Synthetic Flavin Analogue Tan, Zhuotao; Zhu, Chenjie; Fu, Jingwen Angewandte Chemie International Edition, Vol. 57, Issue 50 https://doi.org/10.1002/anie.201810881	journal	November 2018
Switch in Cofactor Specificity of a Baeyer-Villiger Monooxygenase Beier, Andy; Bordewick, Sven; Genz, Maika ChemBioChem, Vol. 17, Issue 24 https://doi.org/10.1002/cbic.201600484	journal	November 2016
Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity Patel, Khushboo M.; Teran, David; Zheng, Shan Chemistry - A European Journal, Vol. 23, Issue 72 https://doi.org/10.1002/chem.201704481	journal	November 2017
In-Silico Bioprospecting: Finding Better Enzymes Kamble, Asmita; Srinivasan, Sumana; Singh, Harinder Molecular Biotechnology, Vol. 61, Issue 1 https://doi.org/10.1007/s12033-018-0132-1	journal	November 2018
Engineering highly functional thermostable proteins using ancestral sequence reconstruction Gumulya, Yosephin; Baek, Jong-Min; Wun, Shun-Jie Nature Catalysis, Vol. 1, Issue 11 https://doi.org/10.1038/s41929-018-0159-5	journal	October 2018
Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+ with Its Application to Biobatteries Chen, Hui; Zhu, Zhiguang; Huang, Rui Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep36311	journal	November 2016
Ultra-rapid rates of water splitting for biohydrogen gas production through in vitro artificial enzymatic pathways Kim, Eui-Jin; Kim, Jae-Eung; Zhang, Yi-Heng P. Job Energy & Environmental Science, Vol. 11, Issue 8 https://doi.org/10.1039/c8ee00774h	journal	January 2018
Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes Cahn, J. K. B.; Baumschlager, A.; Brinkmann-Chen, S. Protein Engineering Design and Selection https://doi.org/10.1093/protein/gzv057	journal	October 2015
Biological Functions of ilvC in Branched-Chain Fatty Acid Synthesis and Diffusible Signal Factor Family Production in Xanthomonas campestris Li, Kai-Huai; Yu, Yong-Hong; Dong, Hui-Juan Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02486	journal	December 2017
Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae Kim, Gyuhee; Shin, Donghyuk; Lee, Sumin Crystals, Vol. 9, Issue 11 https://doi.org/10.3390/cryst9110551	journal	October 2019

Similar Records

Comparative study of the tissue distribution of NADH and NADPH-dependent chloral hydrate reducing enzymes in the rat

Journal Article · Wed Feb 28 23:00:00 EST 1990 · Bulletin of Environmental Contamination and Toxicology; (USA) · OSTI ID:7098759

Oxalyl hydroxamates as reaction-intermediate analogues for ketol-acid reductoisomerase

Journal Article · Mon Mar 19 23:00:00 EST 1990 · Biochemistry; (USA) · OSTI ID:6325456

Engineered microorganisms capable of producing target compounds under anaerobic conditions

Patent · Mon Jan 16 23:00:00 EST 2012 · OSTI ID:1034914

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
branched-chain amino acid pathway
cofactor imbalance

General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH

Citation Formats

References (38)

Cited By (19)

Similar Records

Related Subjects