Walsh, C. T. & Tang, Y. The Chemical Biology of Human Vitamins (RSC, 2019).Percudani, R. & Peracchi, A. A genomic overview of pyridoxal-phosphate-dependent enzymes. EMBO Rep. 4, 850–854 (2003).Article
CAS
PubMed
PubMed Central
Google Scholar
Savile, C. K. et al. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 329, 305–309 (2010).Article
CAS
PubMed
Google Scholar
Phillips, R. S., Poteh, P., Krajcovic, D., Miller, K. A. & Hoover, T. R. Crystal structure of d-ornithine/d-lysine decarboxylase, a stereoinverting decarboxylase: implications for substrate specificity and stereospecificity of fold III decarboxylases. Biochemistry 58, 1038–1042 (2019).Article
CAS
PubMed
Google Scholar
de Chiara, C. et al. d-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition. Nat. Chem. Biol. 16, 686–694 (2020).Article
PubMed
PubMed Central
Google Scholar
Li, Q. et al. Deciphering the biosynthetic origin of l-allo-isoleucine. J. Am. Chem. Soc. 138, 408–415 (2016).Article
CAS
PubMed
Google Scholar
Phillips, R. S., Demidkina, T. V. & Faleev, N. G. Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase. Biochim. Biophys. Acta Proteins Proteom. 1647, 167–172 (2003).Article
CAS
Google Scholar
Sato, D. & Nozaki, T. Methionine gamma-lyase: the unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancers. IUBMB Life 61, 1019–1028 (2009).Article
CAS
PubMed
Google Scholar
Watkins-Dulaney, E., Straathof, S. & Arnold, F. Tryptophan synthase: biocatalyst extraordinaire. ChemBioChem 22, 5–16 (2021).Article
CAS
PubMed
Google Scholar
Hai, Y., Chen, M., Huang, A. & Tang, Y. Biosynthesis of mycotoxin fusaric acid and application of a PLP-dependent enzyme for chemoenzymatic synthesis of substituted l-pipecolic acids. J. Am. Chem. Soc. 142, 19668–19677 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Cui, Z. et al. Pyridoxal-5′-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis. Nat. Chem. Biol. 16, 904–911 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Seebeck, F. P. & Hilvert, D. Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation. J. Am. Chem. Soc. 125, 10158–10159 (2003).Article
CAS
PubMed
Google Scholar
Alexeev, D. et al. The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. J. Mol. Biol. 284, 401–419 (1998).Article
CAS
PubMed
Google Scholar
Du, Y.-L. et al. A pyridoxal phosphate–dependent enzyme that oxidizes an unactivated carbon-carbon bond. Nat. Chem. Biol. 12, 194–199 (2016).Article
CAS
PubMed
Google Scholar
Hoffarth, E. R. et al. A shared mechanistic pathway for pyridoxal phosphate–dependent arginine oxidases. Proc. Natl Acad. Sci. USA 118, e2012591118 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Hoffarth, E. R., Rothchild, K. W. & Ryan, K. S. Emergence of oxygen- and pyridoxal phosphate-dependent reactions. FEBS J. 287, 1403–1428 (2020).Article
CAS
PubMed
Google Scholar
Noguchi, T., Isogai, S., Terada, T., Nishiyama, M. & Kuzuyama, T. Cryptic oxidative transamination of hydroxynaphthoquinone in natural product biosynthesis. J. Am. Chem. Soc. 144, 5435–5440 (2022).Article
CAS
PubMed
Google Scholar
Cordoza, J. L. et al. Mechanistic and structural insights into a divergent PLP-dependent l-enduracididine cyclase from a toxic cyanobacterium. ACS Catal. 13, 9817–9828 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Gao, J. et al. A pyridoxal 5′-phosphate-dependent Mannich cyclase. Nat. Catal. 6, 476–486 (2023).Article
CAS
Google Scholar
Eliot, A. C. & Kirsch, J. F. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73, 383–415 (2004).Article
CAS
PubMed
Google Scholar
Du, Y. L. & Ryan, K. S. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat. Prod. Rep. 36, 430–457 (2019).Article
CAS
PubMed
Google Scholar
Rocha, J. F., Pina, A. F., Sousa, S. F. & Cerqueira, N. M. F. S. A. PLP-dependent enzymes as important biocatalysts for the pharmaceutical, chemical and food industries: a structural and mechanistic perspective. Catal. Sci. Technol. 9, 4864–4876 (2019).Article
CAS
Google Scholar
Ellis, J. M. et al. Biocatalytic synthesis of non-standard amino acids by a decarboxylative aldol reaction. Nat. Catal. 5, 136–143 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Kimura, T., Vassilev, V. P., Shen, G. J. & Wong, C. H. Enzymatic synthesis of β-hydroxy-α-amino acids based on recombinant d- and l-threonine aldolases. J. Am. Chem. Soc. 119, 11734–11742 (1997).Article
CAS
Google Scholar
Barra, L. et al. β-NAD as a building block in natural product biosynthesis. Nature 600, 754–758 (2021).Article
CAS
PubMed
Google Scholar
Hu, Z., Awakawa, T., Ma, Z. & Abe, I. Aminoacyl sulfonamide assembly in SB-203208 biosynthesis. Nat. Commun. 10, 184 (2019).Article
PubMed
PubMed Central
Google Scholar
Barra, L., Awakawa, T. & Abe, I. Noncanonical functions of enzyme cofactors as building blocks in natural product biosynthesis. JACS Au 2, 1950–1963 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 28, 263–266 (2000).Article
CAS
PubMed
PubMed Central
Google Scholar
Harmange Magnani, C. S. & Maimone, T. J. Dearomative synthetic entry into the altemicidin alkaloids. J. Am. Chem. Soc. 143, 7935–7939 (2021).Article
CAS
PubMed
Google Scholar
Fleischman, N. M. et al. Molecular characterization of novel pyridoxal-5′-phosphate-dependent enzymes from the human microbiome. Protein Sci. 23, 1060–1076 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Huai, Q. et al. Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5′-phosphate provide new insight into catalytic mechanisms. J. Biol. Chem. 276, 38210–38216 (2001).Article
CAS
PubMed
Google Scholar
Kelly, R. C. et al. The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA. Nat. Chem. Biol. 5, 891–895 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Jahan, N. et al. Insights into the biosynthesis of the Vibrio cholerae major autoinducer CAI-1 from the crystal structure of the PLP-dependent enzyme CqsA. J. Mol. Biol. 392, 763–773 (2009).Article
CAS
PubMed
Google Scholar
Chen, M., Liu, C. T. & Tang, Y. Discovery and biocatalytic application of a PLP-dependent amino acid γ-substitution enzyme that catalyzes C–C bond formation. J. Am. Chem. Soc. 142, 10506–10515 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Abad, A. N. D. et al. Discovery and characterization of pyridoxal 5′-phosphate-dependent cycloleucine synthases. J. Am. Chem. Soc. 146, 14672–14684 (2024).Article
CAS
PubMed
Google Scholar
Liu, S. et al. Molecular and structural basis for Cγ–C bond formation by PLP‐dependent enzyme Fub7. Angew. Chem. Int. Ed. 63, e202317161 (2024).Article
CAS
Google Scholar
Gherardini, P. F., Ausiello, G., Russell, R. B. & Helmer-Citterich, M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Res. 38, 3809–3816 (2010).Article
CAS
PubMed
PubMed Central
Google Scholar
Sundriyal, A., Roberts, A. K., Shone, C. C. & Acharya, K. R. Structural basis for substrate recognition in the enzymatic component of ADP-ribosyltransferase toxin CDTa from Clostridium difficile. J. Biol. Chem. 284, 28713–28719 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Langelier, M., Adp-ribosyl, P., Planck, J. L., Roy, S. & Pascal, J. M. Structural basis for DNA damage–dependent poly(ADP-ribosyl)ation by human PARP-1. Science 336, 728–733 (2012).Article
CAS
PubMed
PubMed Central
Google Scholar
Alemasova, E. E. & Lavrik, O. I. Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins. Nucleic Acids Res. 47, 3811–3827 (2019).Article
CAS
PubMed
PubMed Central
Google Scholar
Xu, Z., Pan, G., Zhou, H. & Shen, B. Discovery and characterization of 1-aminocyclopropane-1-carboxylic acid synthase of bacterial origin. J. Am. Chem. Soc. 140, 16957–16961 (2018).Article
CAS
PubMed
Google Scholar
Maruyama, C. et al. C-Methylation of S-adenosyl-L-methionine occurs prior to cyclopropanation in the biosynthesis of 1-amino-2-methylcyclopropanecarboxylic acid (Norcoronamic acid) in a bacterium. Biomolecules 10, 775–790 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Mann, S. & Ploux, O. Pyridoxal-5′-phosphate-dependent enzymes involved in biotin biosynthesis: structure, reaction mechanism and inhibition. Biochim. Biophys. Acta Proteins Proteom. 1814, 1459–1466 (2011).Article
CAS
Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Lee, Y.-H., Ren, D., Jeon, B. & Liu, H.-W. S-Adenosylmethionine: more than just a methyl donor. Nat. Prod. Rep. 40, 1521–1549 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Komeda, H., Kobayashi, M. & Shimizu, S. Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proc. Natl Acad. Sci. USA 93, 4267–4272 (1996).Article
CAS
PubMed
PubMed Central
Google Scholar
Tao, H. et al. Discovery of non-squalene triterpenes. Nature 606, 414–419 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).Article
PubMed
PubMed Central
Google Scholar
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).Article
PubMed
PubMed Central
Google Scholar
Mori, T. et al. C-Glycoside metabolism in the gut and in nature: identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat. Commun. 12, 6294 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Zivanov, J., Nakane, T. & Scheres, S. H. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019).Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).Article
CAS
PubMed
PubMed Central
Google Scholar
Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013).Article
CAS
PubMed
PubMed Central
Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).Article
CAS
PubMed
Google Scholar
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).Article
CAS
PubMed
PubMed Central
Google Scholar
Hirakawa, Y. et al. Characterization of a novel type of carbonic anhydrase that acts without metal cofactors. BMC Biol. 19, 105 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Imasaki, T. et al. CAMSAP2 organizes a γ-tubulin-independent microtubule nucleation centre through phase separation. Elife 11, e77365 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).Article
PubMed
Google Scholar
Zhu, W., Shenoy, A., Kundrotas, P. & Elofsson, A. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes. Bioinformatics 39, btad424 (2023).Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Elfmann, C. & Stülke, J. PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks. Nucleic Acids Res. 51, W404–W410 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Case, D. A. et al. Amber 2020 (University of California, San Francisco, 2020).Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015).Article
CAS
PubMed
PubMed Central
Google Scholar
Walker, R. C., de Souza, M. M., Mercer, I. P., Gould, I. R. & Klug, D. R. Large and fast relaxations inside a protein: calculation and measurement of reorganization energies in alcohol dehydrogenase. J. Phys. Chem. B 106, 11658–11665 (2002).Article
CAS
Google Scholar
Pavelites, J. J., Gao, J., Bash, P. A. & Mackerell, A. D. Jr A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides. J. Comput. Chem. 18, 221–239 (1997).Article
CAS
Google Scholar
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general Amber force field. J. Comput. Chem. 25, 1157–1174 (2004).Article
CAS
PubMed
Google Scholar
Bayly, C. I., Cieplak, P., Cornell, W. & Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97, 10269–10280 (1993).Article
CAS
Google Scholar
Frisch, M.J. et al. Gaussian 16 revision B.01 (Gaussian, 2016).Lusiany, T. et al. Enhancement of SARS-CoV-2 infection via crosslinking of adjacent spike proteins by N-terminal domain-targeting antibodies. Viruses 15, 2421 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).Article
CAS
Google Scholar
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).Article
PubMed
Google Scholar
Bernetti, M. & Bussi, G. Pressure control using stochastic cell rescaling. J. Chem. Phys. 153, 114107 (2020).Article
CAS
PubMed
Google Scholar
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).Article
CAS
Google Scholar
Hess, B. P-LINCS: a parallel linear constraint solver for molecular simulation. J. Chem. Theory Comput. 4, 116–122 (2008).Article
CAS
PubMed
Google Scholar
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).Article
CAS
Google Scholar
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).Article
CAS
Google Scholar
Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008).Article
CAS
PubMed
Google Scholar
Vermeeren, P. et al. Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance. Phys. Chem. Chem. Phys. 24, 18028–18042 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao, Y. & Truhlar, D. G. 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, 215–241 (2008).Article
CAS
Google Scholar
Weigend, F. Accurate Coulomb-fitting basis sets for H to Rn. Phys. Chem. Chem. Phys. 8, 1057–1065 (2006).Article
CAS
PubMed
Google Scholar
Weigend, F. & Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys. Chem. Chem. Phys. 7, 3297–3305 (2005).Article
CAS
PubMed
Google Scholar
Marenich, A. V., Cramer, C. J. & Truhlar, D. G. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J. Phys. Chem. B 113, 6378–6396 (2009).Article
CAS
PubMed
Google Scholar
Gonzalez, C. & Schlegel, H. B. Reaction path following in mass-weighted internal coordinates. J. Phys. Chem. 94, 5523–5527 (1990).Article
CAS
Google Scholar
Fukui, K. The path of chemical reactions – the IRC approach. Acc. Chem. Res. 14, 363–368 (1981).Article
CAS
Google Scholar
Maeda, S., Harabuchi, Y., Ono, Y., Taketsugu, T. & Morokuma, K. Intrinsic reaction coordinate: calculation, bifurcation, and automated search. Int. J. Quantum Chem. 115, 258–269 (2015).Article
CAS
Google Scholar