Abstract
Abstract
An Fe-type nitrile hydratase α(ɛ) protein complex from Rhodococcus equi TG328-2 (ReNHase) was discovered and shown by MALDI-TOF to form a 1:1 complex. As isolated, the α(ɛ) protein complex exhibited no detectable NHase activity even in the presence of iron. The addition of the ReNHase β-subunit and Fe(II) to the ReNHase apo-α(ε) complex, provided an enzyme with a kcat value of 0.7 ± 0.1 s−1 using acrylonitrile as the substrate, indicating that the β-subunit is important for the reconstitution of NHase activity. The addition of the reducing agent TCEP enhanced the activity by more than 50% (kcat of 1.7 ± 0.2 s−1). As the (ɛ) protein was previously shown to bind and hydrolyze GTP, the addition of GTP to the as-purified α(ε) complex provided a kcat value of 1.1 ± 0.2 s−1, in the presence of Fe(II) and β-subunit. The addition of TCEP to this combination further enhanced the activity (kcat of 2.1 ± 0.3 s−1). Apo α-subunit was expressed in purified and added to the (ɛ) protein and β-subunits plus Fe(II) and TCEP resulting in a kcat value of 0.7 ± 0.2 s−1 suggesting an α(ɛ) complex can form in vitro. The addition of GTP to this sample increased the observed rate of nitrile hydration by ~ 30%, while TCEP free samples exhibited no activity. Taken together, these data provide insight into the role of the (ɛ) protein and the newly discovered α(ɛ) complex in NHase metallocenter assembly.
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Yamada H, Kobayashi M (1996) Hydratases involved in nitrile conversion: screening, characterization and application. Biosci Biotech Biochem 60:1391–1400
Brady D, Beeton A, Zeevaart J, Kgaje C, van Rantwijk F, Sheldon RA (2004) Characterisation of nitrilase and nitrile hydratase biocatalytic systems. Appl Microbiol Biotechnol 64:76–85
Kovacs JA (2004) Synthetic analogues of cysteinate-ligated non-heme iron and non-corrinoid cobalt enzymes. Chem Rev 104:825–848
Harrop TC, Mascharak PK (2004) Fe(III) and Co(III) centers with carboxamido nitrogen and modified sulfur coordination: lessons learned from nitrile hydratase. Acc Chem Res 37:253–260
Dey A, Chow M, Taniguchi K, Lugo-Mas P, Davin S, Maeda M, Kovacs JA, Odaka M, Hodgson KO, Hedman B, Solomon EI (2006) Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site. J Am Chem Soc 128:533–541
Lu J, Zheng Y, Yamagishi H, Odaka M, Tsujimura M, Maeda M, Endo I (2003) Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo. FEBS Lett 553:391–396
Nishiyama M, Horinouchi S, Kobayashi M, Nagasawa T, Yamada H, Beppu T (1991) Cloning and characterization of genes responsible for metabolism of nitrile compounds from Pseudomonas chlororaphis B23. J Bacteriol 173:2465–2472
Hashimoto Y, Nishiyama M, Horinouchi S, Beppu T (1994) Nitrile hydratase gene from Rhodococcus sp. N-774 requirement for its downstream region for efficient expression. Biosci Biotechnol Biochem 58:1859–1869
Nojiri M, Yohda M, Odaka M, Matsushita Y, Tsujimura M, Yoshida T, Dohmae N, Takio K, Endo I (1999) Functional expression of nitrile hydratase in Escherichia coli: requirement of a nitrile hydratase activator and post-translational modification of a ligand cysteine. J Biochem 125:696–704
Haas C, Rodionov D, Kropat J, Malasarn D, Merchant S, de Crecy-Lagard V (2009) A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 10:470
Cameron RA, Sayed M, Cowan DA (2005) Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus pallidus RAPc8. Biochim Biophys Acta Gen Subj 1725:35–46
Zhou Z, Hashimoto Y, Cui T, Washizawa Y, Mino H, Kobayashi M (2010) Unique biogenesis of high-molecular mass multimeric metalloenzyme nitrile hydratase: intermediates and a proposed mechanism for self-subunit swapping maturation. Biochemistry 49:9638–9648
Zhou Z, Hashimoto Y, Kobayashi M (2009) Self-subunit swapping chaperone needed for the maturation of multimeric metalloenzyme nitrile hydratase by a subunit exchange mechanism also carries out the oxidation of the metal ligand cysteine residues and insertion of cobalt. J Biol Chem 284:14930–14938
Zhou Z, Hashimoto Y, Shiraki K, Kobayashi M (2008) Discovery of posttranslational maturation by self-subunit swapping. Proc Natl Acad Sci 105:14849–14854
Cheng T, Li H, Yang X, Xia W, Sun H (2013) Interaction of SlyD with HypB of Helicobacter pylori facilitates nickel trafficking. Metallomics 5:804–807
Gumataotao N, Lankathilaka KPW, Bennett B, Holz RC (2017) The iron-type nitrile hydratase activator protein is a GTPase. Biochemical Journal 474:247–258
Sydor AM, Jost M, Ryan KS, Turo KE, Douglas CD, Drennan CL, Zamble DB (2013) Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases. Biochemistry 52:1788–1801
Rzeznicka K, Schatzle S, Bottcher D, Klein J, Bornscheuer UT (2010) Cloning and functional expression of a nitrile hydratase (NHase) from Rhodococcus equi TG328-2 in Escherichia coli, its purification and biochemical characterisation. Appl Microbiol Biotechnol 85:1417–1425
Blaby-Haas CE, Flood JA, Crécy-Lagard VD, Zamble DB (2012) YeiR: a metal-binding GTPase from Escherichia coli involved in metal homeostasis. Metallomics Integr Biometal Sci 4:488–497
Song BD, Schmid SL (2003) A molecular motor or a regulator? Dynamin’s in a class of its own. Biochemistry 42:1369–1376
Nelp MT, Astashkin AV, Breci LA, McCarty RM, Bandarian V (2014) The alpha subunit of nitrile hydratase is sufficient for catalytic activity and post-translational modification. Biochemistry 53:3990–3994
Yamaguchi H, Miyazaki M (2014) Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies. Biomolecules 4:235–251
Kuhn ML, Martinez S, Gumataotao N, Bornscheuer U, Liu D, Holz RC (2012) The Fe-type nitrile hydratase from Comamonas testosteroni Ni1 does not require an activator accessory protein for expression in Escherichia coli. Biochem Biophys Res Commun 424:365–370
Miyanaga A, Fushinobu S, Ito K, Shoun H, Wakagi T (2004) Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding. Eur J Biochem 271:429–438
Piersma SR, Nojiri M, Tsujimura M, Noguchi T, Odaka M, Yohda M, Inoue Y, Endo I (2000) Arginine 56 mutation in the beta subunit of nitrile hydratase: importance of hydrogen bonding to the non-heme iron center. J Inorg Biochem 80:283–288
Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M (2015) Time-resolved crystallography of the reaction intermediate of nitrile hydratase: revealing a role for the cysteine sulfenic acid ligand as a catalytic nucleophile. Angew Chem Int Ed Engl 54:10763–10767
Yamanaka Y, Hashimoto K, Ohtaki A, Noguchi K, Yohda M, Odaka M (2010) Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase. J Biol Inorg Chem 15:655–665
Miyanaga A, Fushinobu S, Ito K, Wakagi T (2001) Crystal structure of cobalt-containing nitrile hydratase. Biochem Biophys Res Commun 288:1169–1174
Acknowledgments
We thank the National Science Foundation (CHE-1808711, RCH & BB) for funding this research.
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This work was supported by the National Science Foundation (CHE-1808711 BB & RCH), the Todd Wehr Foundation, and Bruker Biospin.
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KPWL prepared expression plasmid, carried out protein expression, purification, enzymatic assays and prepared samples for metal analysis, and analyzed the results. RCH conceived of the idea and wrote the paper with KPWL and BB.
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Lankathilaka, K.P.W., Bennett, B. & Holz, R.C. The Fe-type nitrile hydratase from Rhodococcus equi TG328-2 forms an alpha-activator protein complex. J Biol Inorg Chem 25, 903–911 (2020). https://doi.org/10.1007/s00775-020-01806-y
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DOI: https://doi.org/10.1007/s00775-020-01806-y