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Russell H, Stewart R, Prior C, Oganesyan VS, Gaule TG, Lovett JE. DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis. APPLIED MAGNETIC RESONANCE 2021; 52:995-1015. [PMID: 34720439 PMCID: PMC8550341 DOI: 10.1007/s00723-021-01321-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 03/10/2021] [Indexed: 06/13/2023]
Abstract
In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin-spin distances at nanometre-scale by measuring dipole-dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01321-6.
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Affiliation(s)
- Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | - Rachel Stewart
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | | | | | - Thembaninkosi G. Gaule
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Janet E. Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
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Gaule TG, Smith MA, Pearson AR, Knowles PF, McPherson MJ. Probing the molecular mechanisms in copper amine oxidases by generating heterodimers. Chembiochem 2015; 16:559-64. [PMID: 25607656 PMCID: PMC4497604 DOI: 10.1002/cbic.201402653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 11/29/2022]
Abstract
For some homodimeric copper amine oxidases (CuAO), there is suggestive evidence of differential activity at the two active sites implying potential cooperativity between the two monomers. To examine this phenomenon for the Arthrobacter globiformis CuAO (AGAO), we purified a heterodimeric form of the enzyme for comparison with the homodimer. The heterodimer comprises an active wild-type monomer and an inactive monomer in which an active-site tyrosine is mutated to phenylalanine (Y382F). This mutation prevents the formation of the trihydroxyphenylalanine quinone (TPQ) cofactor. A pETDuet vector and a dual fusion tag strategy was used to purify heterodimers (WT/Y382F) from homodimers. Purity was confirmed by western blot and native PAGE analyses. Spectral and kinetic studies support the view that whether there are one or two functional monomers in the dimer, the properties of each functional monomer are the same, thus indicating no communication between the active sites in this bacterial enzyme.
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Affiliation(s)
- Thembaninkosi G Gaule
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT Leeds (UK) E-mail:
| | - Mark A Smith
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT Leeds (UK) E-mail:
| | - Arwen R Pearson
- Hamburg Centre of Ultrafast Imaging, University of Hamburg, CFELBuilding 99, Luruper Chausse 149, 22761 Hamburg (Germany)
| | - Peter F Knowles
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT Leeds (UK) E-mail:
| | - Michael J McPherson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT Leeds (UK) E-mail:
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1129] [Impact Index Per Article: 112.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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Murakawa T, Hayashi H, Sunami T, Kurihara K, Tamada T, Kuroki R, Suzuki M, Tanizawa K, Okajima T. High-resolution crystal structure of copper amine oxidase fromArthrobacter globiformis: assignment of bound diatomic molecules as O2. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2483-94. [DOI: 10.1107/s0907444913023196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/18/2013] [Indexed: 11/10/2022]
Abstract
The crystal structure of a copper amine oxidase fromArthrobacter globiformiswas determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographicRfactor andRfreewere 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overallBfactor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70 000. About 40% of the presumed H atoms were observed as clear electron densities in theFo−Fcdifference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.
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Foster A, Barnes N, Speight R, Keane MA. Identification, functional expression and kinetic analysis of two primary amine oxidases from Rhodococcus opacus. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Langley DB, Trambaiolo DM, Duff AP, Dooley DM, Freeman HC, Guss JM. Complexes of the copper-containing amine oxidase from Arthrobacter globiformis with the inhibitors benzylhydrazine and tranylcypromine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:577-83. [PMID: 18607080 PMCID: PMC2443983 DOI: 10.1107/s174430910801556x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 05/23/2008] [Indexed: 11/10/2022]
Abstract
Complexes of Arthrobacter globiformis amine oxidase (AGAO) with the inhibitors benzylhydrazine and tranylcypromine (an antidepressant drug) have been refined at 1.86 and 1.65 A resolution, respectively. Both inhibitors form covalent adducts with the TPQ cofactor. A tyrosine residue, proposed to act as a gate to the AGAO active site, is in its open conformation.
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Affiliation(s)
- David B Langley
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
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Langley DB, Brown DE, Cheruzel LE, Contakes SM, Duff AP, Hilmer KM, Dooley DM, Gray HB, Guss JM, Freeman HC. Enantiomer-specific binding of ruthenium(II) molecular wires by the amine oxidase of Arthrobacter globiformis. J Am Chem Soc 2008; 130:8069-78. [PMID: 18507382 PMCID: PMC2518534 DOI: 10.1021/ja801289f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The copper amine oxidase from Arthrobacter globiformis (AGAO) is reversibly inhibited by molecular wires comprising a Ru(II) complex head group and an aromatic tail group joined by an alkane linker. The crystal structures of a series of Ru(II)-wire-AGAO complexes differing with respect to the length of the alkane linker have been determined. All wires lie in the AGAO active-site channel, with their aromatic tail group in contact with the trihydroxyphenylalanine quinone (TPQ) cofactor of the enzyme. The TPQ cofactor is consistently in its active ("off-Cu") conformation, and the side chain of the so-called "gate" residue Tyr296 is consistently in the "gate-open" conformation. Among the wires tested, the most stable complex is produced when the wire has a -(CH2)4- linker. In this complex, the Ru(II)(phen)(bpy)2 head group is level with the protein molecular surface. Crystal structures of AGAO in complex with optically pure forms of the C4 wire show that the linker and head group in the two enantiomers occupy slightly different positions in the active-site channel. Both the Lambda and Delta isomers are effective competitive inhibitors of amine oxidation. Remarkably, inhibition by the C4 wire shows a high degree of selectivity for AGAO in comparison with other copper-containing amine oxidases.
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Affiliation(s)
- David B. Langley
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Doreen E. Brown
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Lionel E. Cheruzel
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen M. Contakes
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Kimberly M. Hilmer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - J. Mitchell Guss
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Hans C. Freeman
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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