Crystal structure of 4-hydroxybutyryl-CoA synthetase (ADP-former) from nitrosopumilus maritimus

Friedlingstein P. et al. Uncertainties in CMIP5 climate projections due to carbon cycle feedback. J. Klim. 27511–526 (2014).

Google Scholar article

Berg I.A. Ecological aspects of the distribution of various autotrophic COs₂ fixation paths. Adj. Environment. Microbiol. 771925–1936 (2011).

CAS article PubMed PubMed Central Google Scholar

Ducat, DC and Silver, PA Improving carbon fixation pathways. Well. Opinion. chem. Biol. 16337–344 (2012).

CAS article PubMed PubMed Central Google Scholar

Berg I.A., Ramos-Vera V.H., Petri A., Huber H. and Fuchs G. Study of autotrophic CO distribution₂ fixation cycles in Crenarchaeota. Microbiology 156256–269 (2009).

Article PubMed Google Scholar

Herter, S., Fuchs, G., Bacher, A. and Eisenreich, W. Bicyclic autotrophic CO.₂ Pathway of fixation in chromoflexus aurantiacus. J. Biol. chem. 27720277–20283 (2002).

CAS article PubMed Google Scholar

Huber, H. et al. The autotrophic dicarboxylate/4-hydroxybutyrate carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Textbook Natl Acad. Sci. 1057851–7856 (2008).

CAS article PubMed PubMed Central Google Scholar

Sanchez-Andrea I. et al. The reductive glycine pathway mediates autotrophic growth of Desulfovibrio desulfuricans. Nat. Commun. 11, https://doi.org/10.1038/s41467-020-18906-7 (2020).

Kenneke M. et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO release.₂ fixation. Textbook Natl. acad. Sci. 1118239–8244 (2014).

Article PubMed PubMed Central Google Scholar

Ingalls, A.E. et al. Quantitative assessment of autotrophy of an archaeal community in the mesopelagic ocean using natural radiocarbon. Textbook Natl. acad. Sci. 1036442–6447 (2006).

CAS article PubMed PubMed Central Google Scholar

Hawkins, A.B. et al. Bioprocessing Analysis of Pyrococcus Furiosus Strains Engineered for CO₂based on the production of 3-hydroxypropionate. Biotechnology. Bioeng. 1121533–1543 (2015).

CAS article PubMed PubMed Central Google Scholar

Berg, I. A., Kockelkorn, D., Bakel, W. and Fuchs, G. The autotrophic 3-hydroxypropionate/4-hydroxybutyrate carbon dioxide assimilation pathway in archaea. Science 3181782–1786 (2007).

CAS article PubMed Google Scholar

Alber, B.E., Kung, J.W. and Fuchs, G. 3-hydroxypropionyl coenzyme A synthetase from Metallosphaera sedula, an enzyme involved in autotrophic CO.₂ fixation. J. Bacteriol. 1901383–1389 (2007).

Article PubMed PubMed Central Google Scholar

Ramos-Vera, V.H., Weiss, M., Strittmatter, E., Kockelkorn, D. and Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 1931201–1211 (2010).

Article PubMed PubMed Central Google Scholar

Hawkins A.S., Han Y.-T., Bennett R.C., Adams M.W.W. and Kelly R.M. Role of 4-hydroxybutyrate-CoA synthetase in CO₂ The fixation cycle in thermoacidophilic archaea. J. Biol. chem. 2884012–4022 (2013).

CAS article PubMed Google Scholar

Loder, A.J. and Han et al. Analysis of the reaction kinetics of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea. Metab. English 38446–463 (2016).

CAS article PubMed PubMed Central Google Scholar

Berg, P. and Newton, G. Acyl adenylates: an enzymatic mechanism for acetate activation. J. Biol. chem. 222991–1013 (1956).

CAS article PubMed Google Scholar

Berg, P. Acyl adenylates; synthesis and properties of adenyl acetate. J. Biol. chem. 2221015–1023, https://pubmed.ncbi.nlm.nih.gov/13367068/ (1956).

CAS article PubMed Google Scholar

Brazen, K., Schmidt, M., Grotzinger, J. and Schönheit, P. Reaction mechanism and structural model of ADP-forming acetyl-CoA synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. chem. 28315409–15418 (2008).

Article PubMed PubMed Central Google Scholar

Fraser, M.E., James, M.N.H., Bridger, V.A. and Volodko, V.T. Detailed structural description of Escherichia coli11 succinyl-CoA synthetase. Edited by D. Rees. J. Mol. Biol. 285163998.2324 (1999).

Google Scholar article

Weisse, R.H.J., Faust, A., Schmidt, M., Schönheit, P., and Scheidig, A.J. The structure of the NDP-forming acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Textbook Natl Acad. Sci. 113E519–E528 (2016).

Article PubMed PubMed Central Google Scholar

Volodko V.T., Fraser M.E., James M.N. and Bridger W.A. Crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5 Å resolution. J. Biol. chem. 26910883–10890 (1994).

CAS article PubMed Google Scholar

Hohl, W.G.J., Duinen, van and Berendsen, H.J.K. α-helix dipole and properties of proteins. Nature 273443–446 (1978).

Article PubMed Google Scholar

Thompson, M.J. and Eisenberg, D. Transproteomic evidence for a mechanism of loop deletion to increase protein thermostability. J. Mol. Biol. 290595–604 (1999).

CAS article PubMed Google Scholar

Sorensen, B.R., Faga, L.A., Hultman, R., and Shea, M.A. The interdomain linker increases the thermostability and reduces the calcium affinity of the calmodulin N domain. Biochemistry 4115–20 (2001).

Google Scholar article

Sanchez, L.B., Galperin, M.Yu. and Müller, M. Acetyl-CoA synthetase from the amitochondrial eukaryote Giardia belongs to the recently recognized superfamily of acyl-CoA synthetases (nucleoside diphosphate-forming). J. Biol. chem. 275, 5794–5803 2000).

Elkins, J.G. etc. The korarchaeal genome provides insight into the evolution of archaea. Textbook Natl. acad. Sci. 1058102–8107 (2008).

CAS article PubMed PubMed Central Google Scholar

Qin, W. et al. Nitrosopumilus maritimus gen. November, sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov. and Nitrosopumilus ureiphilus sp. nov., four ammonia-oxidizing marine archaea from the phylum Thaumarchaeota. Int. J. Syst. Evolute. Microbiol. 675067–5079 (2017).

Google Scholar article

Lopez-Garcia P, Zivanovic Y, Deschamps P and Moreira D. Bacterial gene import and mesophilic adaptation in archaea. Nat. Rev. Microbiol. 13447–456 (2015).

Article PubMed PubMed Central Google Scholar

Fan, F. et al. On the catalytic mechanism of human ATP-citrate lyase. Biochemistry 515198–5211 (2012).

CAS article PubMed Google Scholar

Atalay N. et al. Cryogenic X-ray crystallographic studies of biomacromolecules on the Turkish light source “Turkish Delight”. Turetsky J. Biol. 471–13 (2023).

CAS Google Scholar article

Kabsh, V. XDS. Acta Crystallogr. Sect. D: Biol. Crystallogr. 66125–132 (2010).

CAS Google Scholar article

Lee, K.-Y. et al. A new ATP-dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA. ELlife10. https://doi.org/10.7554/elife.64045 (2021).

Adams, P.D. et al. PHENIX: a comprehensive Python-based system for solving the structure of macromolecules. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66213–221 (2010).

CAS Google Scholar article

Emslie, P. and Coutan, K. Coote: Modeling tools for molecular graphics. Acta Crystallogr. Sect. D. Biol. Crystallogr. 602126–2132 (2004).

Google Scholar article

Tamura, K. et al. MEGA5: Molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evolution 282731–2739 (2011).

CAS Google Scholar article

Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-based gap penalties, and weight matrix selection. Nucleic Acids Res. 224673–4680 (1994).

CAS article PubMed Google Scholar

Letunik, I. and Bork, P. Interactive Tree of Life (iTOL) v5: an online tool for displaying and annotating a phylogenetic tree. Nucleic Acids Res. 49W293–W296 (2021).

CAS article PubMed PubMed Central Google Scholar

Yariv B. et al. Using evolutionary data to understand macromolecules using an “updated” ConSurf. Protein Science. https://doi.org/10.1002/pro.4582 (2023).

Karner M.B., DeLong E.F. and Karl D.M. Dominance of archaea in the mesopelagic zone of the Pacific Ocean. Nature 409507–510 (2001).

CAS article PubMed Google Scholar

Santoro A.E., Casciotti K.L. and Francis K.A. Activity, abundance, and diversity of nitrifying archaea and bacteria in the central California Current. Environment. Microbiol. 121989–2006 (2010)

CAS article PubMed Google Scholar

Wuchter S. et al. Archaeal nitrification in the ocean. Textbook Natl. acad. Sci. 10312317–12322 (2006).

CAS article PubMed PubMed Central Google Scholar

Zahn, M. et al. Structures of 2-hydroxyisobutyric acid-CoA ligase reveal determinants of substrate specificity and describe a multiconformational catalytic cycle. J. Mol. Biol. 4312747–2761 (2019).

CAS article PubMed Google Scholar

Destan E. et al. Structural information on bifunctional crotonyl-CoA hydratase from thaumarchaea and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Sci. Representative 11 https://doi.org/10.1038/s41598-021-02180-8 (2021).

De Mirchi, H. et al. Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key archaeal carbon fixation enzyme. BioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/2020.02.05.935528 (2020).

Huang J. and Fraser Meng Succinate is bound to porcine GTP-specific succinyl-CoA synthetase. https://doi.org/10.2210/pdb5cae/pdb (2016).

Verschueren, K.H. and others. The structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. Nature 568571–575 (2019).

CAS article PubMed Google Scholar