Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase

Structure

Volumn 22, Issue 7, 2014, Pages 1028-1036

  Kung, Yan ^a,b,c   McAndrew, Ryan P ^a,b   Xie, Xinkai ^a,b   Liu, Charlie C ^d   Pereira, Jose H ^a,b   Adams, Paul D ^a,b,e   Keasling, Jay D ^a,b,d,e  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b JOINT BIOENERGY INSTITUTE   (United States)

^c BRYN MAWR COLLEGE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DITERPENE; GERANYLGERANYL REDUCTASE; ISOPRENOID; OXIDOREDUCTASE; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; GERANYLGERANYL PYROPHOSPHATE; ISOPRENOID PHOSPHATE; PROTEIN BINDING; TERPENE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; HYDROGENATION; LIGAND BINDING; LIPID ANALYSIS; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; REDUCTION; SULFOLOBUS ACIDOCALDARIUS; SYNTHETIC BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MUTATION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

ARCHAEA; SULFOLOBUS ACIDOCALDARIUS;

ARCHAEAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; KINETICS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MUTATION; OXIDOREDUCTASES; POLYISOPRENYL PHOSPHATES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; SULFOLOBUS ACIDOCALDARIUS; TERPENES;

EID: 84904173719     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.05.007     Document Type: Article

References (21)

1. P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.-W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
2. P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, M. Mustyakimov, T.C. Terwilliger, A. Urzhumtsev, P.H. Zwart, and P.D. Adams Towards automated crystallographic structure refinement with phenix.refine Acta Crystallogr. D Biol. Crystallogr. 68 2012 352 367
3. P.K. Ajikumar, W.H. Xiao, K.E.J. Tyo, Y. Wang, F. Simeon, E. Leonard, O. Mucha, T.H. Phon, B. Pfeifer, and G. Stephanopoulos Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli Science 330 2010 70 74
4. H. Alper, K. Miyaoku, and G. Stephanopoulos Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets Nat. Biotechnol. 23 2005 612 616
5. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
6. V.B. Chen, W.B. Arendall III, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
7. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
8. W.R. Farmer, and J.C. Liao Improving lycopene production in Escherichia coli by engineering metabolic control Nat. Biotechnol. 18 2000 533 537
9. J. Jancarik, and S.-H. Kim Sparse matrix sampling: a screening method for crystallization of proteins J. Appl. Crystallogr. 24 1991 409 411
10. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
11. Y. Nishimura, and T. Eguchi Biosynthesis of archaeal membrane lipids: digeranylgeranylglycerophospholipid reductase of the thermoacidophilic archaeon Thermoplasma acidophilum J. Biochem. 139 2006 1073 1081
12. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
13. J. Painter, and E.A. Merritt TLSMD web server for the generation of multi-group TLS models J. Appl. Crystallogr. 39 2006 109 111
14. P.P. Peralta-Yahya, M. Ouellet, R. Chan, A. Mukhopadhyay, J.D. Keasling, and T.S. Lee Identification and microbial production of a terpene-based advanced biofuel Nat. Commun. 2 2011 483
15. N.S. Renninger, and D.J. McPhee Fuel compositions comprising farnesane and farnesane derivatives and method of making and using same U.S. patent July 2008 7,399,323
16. D.-K. Ro, E.M. Paradise, M. Ouellet, K.J. Fisher, K.L. Newman, J.M. Ndungu, K.A. Ho, R.A. Eachus, T.S. Ham, and J. Kirby et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast Nature 440 2006 940 943
17. D. Sasaki, M. Fujihashi, Y. Iwata, M. Murakami, T. Yoshimura, H. Hemmi, and K. Miki Structure and mutation analysis of archaeal geranylgeranyl reductase J. Mol. Biol. 409 2011 543 557
18. S. Sato, M. Murakami, T. Yoshimura, and H. Hemmi Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product J. Bacteriol. 190 2008 3923 3929
19. T.C. Terwilliger Automated main-chain model building by template matching and iterative fragment extension Acta Crystallogr. D Biol. Crystallogr. 59 2003 38 44
20. M.D. Winn, M.N. Isupov, and G.N. Murshudov Use of TLS parameters to model anisotropic displacements in macromolecular refinement Acta Crystallogr. D Biol. Crystallogr. 57 2001 122 133
21. Q. Xu, T. Eguchi, I.I. Mathews, C.L. Rife, H.-J. Chiu, C.L. Farr, J. Feuerhelm, L. Jaroszewski, H.E. Klock, and M.W. Knuth et al. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids J. Mol. Biol. 404 2010 403 417