Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction
Tài liệu tham khảo
Batista-Silva, 2020, Engineering-improved photosynthesis in the era of synthetic biology, Plant Communications, 10.1016/j.xplc.2020.100032
Raines, 2022, Improving carbon fixation, 175
Hawkins, 2011, Extremely thermophilic routes to microbial electrofuels, ACS Catal., 1, 1043, 10.1021/cs2003017
Claassens, 2016, Harnessing the power of microbial autotrophy, Nat. Rev. Microbiol., 14, 10.1038/nrmicro.2016.130
Berg, 2011, Ecological aspects of the distribution of different autotrophic CO2 fixation pathways, Appl. Environ. Microbiol., 77, 1925, 10.1128/AEM.02473-10
Zarzycki, 2009, Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus, Proc. Natl. Acad. Sci. U.S.A., 106, 21317, 10.1073/pnas.0908356106
Werpy, 2004, Top value added chemicals from Biomass Volume I–results of screening for PotentialCandidates from sugars and synthesis gas, p.15 US Dept. of Energy
Bozell, 2010, Technology development for the production of biobased products from biorefinery carbohydrates—the US Department of Energy's ” Top 10” revisited, Green Chem., 12, 539, 10.1039/b922014c
Scheffen, 2021, A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation, Nat. Catal., 4, 105, 10.1038/s41929-020-00557-y
Alber, 2006, Malonyl-coenzyme A reductase in the modified 3-hydroxypropionate cycle for autotrophic carbon fixation in archaeal Metallosphaera and Sulfolobus spp, J. Bacteriol., 188, 8551, 10.1128/JB.00987-06
Liu, 2013, Dissection of malonyl-coenzyme A reductase of Chloroflexus aurantiacus results in enzyme activity improvement, PLoS One, 8
Son, 2020, Structural insight into bi-functional malonyl-CoA reductase, Environ. Microbiol., 22, 752, 10.1111/1462-2920.14885
Kabasakal, 2023, 2023
Zhang, 2023
Ahn, 2023, Cryo-EM structure of bifunctional malonyl-CoA reductase from Chloroflexus aurantiacus reveals a dynamic domain movement for high enzymatic activity, Int. J. Biol. Macromol., 242, 10.1016/j.ijbiomac.2023.124676
Michoux, 2014, Crystal structure of CyanoQ from the thermophilic cyanobacterium Thermosynechococcus elongatus and detection in isolated photosystem II complexes, Photosynth. Res., 122, 57, 10.1007/s11120-014-0010-z
Gibson, 2011, Enzymatic assembly of overlapping DNA fragments, 349, 10.1016/B978-0-12-385120-8.00015-2
Hanahan, 1983, Studies on transformation of Escherichia coli with plasmids, J. Mol. Biol., 166, 557, 10.1016/S0022-2836(83)80284-8
Zhao, 2007, Selenomethionine protein labeling using the Escherichia coli strain KRX, Promega Notes, 96, 24
Kabsch, 2010, XDS, Acta Crystallographica Section D: Biological Crystallography, 66, 125, 10.1107/S0907444909047337
Waterman, 2016, Diffraction-geometry refinement in the DIALS framework, Acta Crystallographica Section D Structural Biology, 72, 558, 10.1107/S2059798316002187
Sheldrick, 2007, A short history of SHELX, Acta Crystallogr., Sect. A: Found. Crystallogr., 64, 112, 10.1107/S0108767307043930
Cowtan, 2006, The Buccaneer software for automated model building. 1. Tracing protein chains, Acta Crystallogr. Sect. D Biol. Crystallogr., 62, 1002, 10.1107/S0907444906022116
Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. Sect. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158
Murshudov, 2011, REFMAC5 for the refinement of macromolecular crystal structures, Acta Crystallogr. Sect. D Biol. Crystallogr., 67, 355, 10.1107/S0907444911001314
Afonine, 2018, Real-space refinement in PHENIX for cryo-EM and crystallography, Acta Crystallogr. D: Struct. Biol., 10.1107/S2059798318006551
McCoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206
Ness, 2004, Crank: new methods for automated macromolecular crystal structure solution, Structure, 12, 1753, 10.1016/j.str.2004.07.018
Pannu, 2011, Recent advances in the CRANK software suite for experimental phasing, Acta Crystallogr. Sect. D Biol. Crystallogr., 67, 331, 10.1107/S0907444910052224
Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073
Schrödinger, 2015
Jumper, 2021, Highly accurate protein structure prediction with AlphaFold, Nature, 596, 583, 10.1038/s41586-021-03819-2
Mirdita, 2022, ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1
Jörnvall, 1995, Short-chain dehydrogenases/reductases (SDR), Biochemistry, 34, 6003, 10.1021/bi00018a001
Persson, 2008, Medium- and short-chain dehydrogenase/reductase gene and protein families: the MDR superfamily, Cell. Mol. Life Sci., 65, 3879, 10.1007/s00018-008-8587-z
Son, 2020, Structural insight into bi-functional malonyl-CoA reductase, Environ. Microbiol., 22, 10.1111/1462-2920.14885
Flamholz, 2012, EQuilibrator - the biochemical thermodynamics calculator, Nucleic Acids Res., 40, 10.1093/nar/gkr874
Haines, 2013, The increasingly complex mechanism of HMG-CoA reductase, Accounts Chem. Res., 46, 10.1021/ar3003267
Demmer, 2013, Structural basis for a bispecific NADP+ and CoA binding site in an archaeal malonyl-coenzyme a reductase, J. Biol. Chem., 288, 6363, 10.1074/jbc.M112.421263
Beck, 2002, The hidden steps of domain skipping: macrolactone ring size determination in the pikromycin modular polyketide synthase, Chem. Biol., 9, 575, 10.1016/S1074-5521(02)00146-1
Varadi, 2022, AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Res., 50, D439, 10.1093/nar/gkab1061
Liu, 2016, Functional balance between enzymes in malonyl-CoA pathway for 3-hydroxypropionate biosynthesis, Metab. Eng., 34, 10.1016/j.ymben.2016.01.001