Origins of stereoselectivity in evolved ketoreductases

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 51, 2015, Pages E7065-E7072

  Noey, Elizabeth L ^a   Tibrewal, Nidhi ^b   Jiménez Osés, Gonzalo ^a   Osuna, Sílvia ^a   Park, Jiyong ^a   Bond, Carly M ^b   Cascio, Duilio ^a   Liang, Jack ^c   Zhang, Xiyun ^c   Huisman, Gjalt W ^c   Tang, Yi ^a,b   Houk, Kendall N ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California   (United States)

^c R and D Project Development and Management   (United States)

Author keywords

Crystallographic structures; Directed evolution; Enantioselectivity; Molecular dynamics; Theozyme

Indexed keywords

KETOREDUCTASE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; OXIDOREDUCTASE; SULOPENEM; UNCLASSIFIED DRUG; WATER; ALCOHOL DEHYDROGENASE; BACTERIAL PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENANTIOMERIC RATIO; ENANTIOSELECTIVITY; ENZYME SUBSTRATE COMPLEX; MOLECULAR DYNAMICS; PRIORITY JOURNAL; STEREOCHEMISTRY; AMINO ACID SUBSTITUTION; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYMOLOGY; GENETICS; KINETICS; LACTOBACILLUS; METABOLISM; MOLECULAR MODEL; PROTEIN CONFORMATION; QUANTUM THEORY; SITE DIRECTED MUTAGENESIS; STEREOISOMERISM; X RAY CRYSTALLOGRAPHY;

ALCOHOL OXIDOREDUCTASES; AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DIRECTED MOLECULAR EVOLUTION; ENZYME STABILITY; KINETICS; LACTOBACILLUS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; QUANTUM THEORY; STEREOISOMERISM; SUBSTRATE SPECIFICITY;

EID: 84952705870     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1507910112     Document Type: Article

References (27)

1. Moore JC, Pollard DJ, Kosjek B, Devine PN (2007) Advances in the enzymatic reduction of ketones. Acc Chem Res 40(12):1412-1419.
2. Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M (2011) Application of designed enzymes in organic synthesis. Chem Rev 111(7):4141-4164.
3. Huisman GW, Liang J, Krebber A (2010) Practical chiral alcohol manufacture using ketoreductases. Curr Opin Chem Biol 14(2):122-129.
4. Bornscheuer UT, et al. (2012) Engineering the third wave of biocatalysis. Nature 485(7397):185-194.
5. Quallich GJ, Woodall TM (1993) Enantioselective oxazaborolidine reduction of ketones containing heteroatoms. Tetrahedron Lett 34(5):785-788.
6. Zhang X, et al. (1993) Asymmetric hydrogenation of cycloalkanones catalyzed by BINAP-iridium (I)-aminophosphine systems. J Am Chem Soc 115(8):3318-3319.
7. Oppermann U, et al. (2003) Short-chain dehydrogenases/reductases (SDR): The 2002 update. Chem Biol Interact 143-144(0):247-253.
8. Weckbecker A, Hummel W (2006) Cloning, expression, and characterization of an (R)-specific alcohol dehydrogenase from Lactobacillus kefir. Biocatalysis Biotransform 24(5):380-389.
9. Filling C, et al. (2002) Critical residues for structure and catalysis in short-chain dehydrogenases/reductases. J Biol Chem 277(28):25677-25684.
10. 2+-dependent dimerization mode. Structure 10(6):773-786.
11. Thoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM (2000) Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase. Biochemistry 39(19):5691-5701.
12. Schlieben NH, et al. (2005) Atomic resolution structures of R-specific alcohol dehydrogenase from Lactobacillus brevis provide the structural bases of its substrate and cosubstrate specificity. J Mol Biol 349(4):801-813.
13. Niefind K, Müller J, Riebel B, Hummel W, Schomburg D (2003) The crystal structure of R-specific alcohol dehydrogenase from Lactobacillus brevis suggests the structural basis of its metal dependency. J Mol Biol 327(2):317-328.
14. Benach J, Atrian S, Gonzàlez-Duarte R, Ladenstein R (1999) The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: Observation of an enzymebound NAD-ketone adduct at 1.4-Å resolution by X-ray crystallography. J Mol Biol 289(2):335-355.
15. Medina JM, Mackey JL, Garg NK, Houk KN (2014) The role of aryne distortions, steric effects, and charges in regioselectivities of aryne reactions. J Am Chem Soc 136(44):15798-15805.
16. Jiménez-Osés G, et al. (2014) The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol 10(6):431-436.
17. Pauling L (1948) Nature of forces between large molecules of biological interest. Nature 161(4097):707-709.
18. Smith AJT, et al. (2008) Structural reorganization and preorganization in enzyme active sites: Comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. J Am Chem Soc 130(46):15361-15373.
19. Yang W, et al. (2009) Free-energy perturbation simulation on transition states and redesign of butyrylcholinesterase. Biophys J 96(5):1931-1938.
20. Wijma HJ, et al. (2015) Enantioselective enzymes by computational design and in silico screening. Angew Chem Int Ed Engl 54(12):3726-3730.
21. Frisch MJ, et al. (2009) Gaussian 09, revision D.01 (Gaussian, Inc., Wallingford, CT).
22. Tao J, Perdew JP, Staroverov VN, Scuseria GE (2003) Climbing the density functional ladder: Nonempirical meta-generalized gradient approximation designed for molecules and solids. Phys Rev Lett 91(14):146401.
23. Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24(6):669-681.
24. Zhao Y, Truhlar D (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Acc 120(1-3):215-241.
25. Case DA, et al. (2012) Amber 12 (University of California, San Francisco).
26. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
27. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21(12):1049-1074.