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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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2
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Teanphonkrang S, Janke S, Chaiyen P, Sucharitakul J, Suginta W, Khunkaewla P, Schuhmann W, Ruff A, Schulte A. Tuned Amperometric Detection of Reduced β-Nicotinamide Adenine Dinucleotide by Allosteric Modulation of the Reductase Component of the p-Hydroxyphenylacetate Hydroxylase Immobilized within a Redox Polymer. Anal Chem 2018; 90:5703-5711. [PMID: 29633834 DOI: 10.1021/acs.analchem.7b05467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the fabrication of an amperometric NADH biosensor system that employs an allosterically modulated bacterial reductase in an adapted osmium(III)-complex-modified redox polymer film for analyte quantification. Chains of complexed Os(III) centers along matrix polymer strings make electrical connection between the immobilized redox protein and a graphite electrode disc, transducing enzymatic oxidation of NADH into a biosensor current. Sustainable anodic signaling required (1) a redox polymer with a formal potential that matched the redox switch of the embedded reductase and avoided interfering redox interactions and (2) formation of a cross-linked enzyme/polymer film for stable biocatalyst entrapment. The activity of the chosen reductase is enhanced upon binding of an effector, i.e. p-hydroxy-phenylacetic acid ( p-HPA), allowing the acceleration of the substrate conversion rate on the sensor surface by in situ addition or preincubation with p-HPA. Acceleration of NADH oxidation amplified the response of the biosensor, with a 1.5-fold increase in the sensitivity of analyte detection, compared to operation without the allosteric modulator. Repetitive quantitative testing of solutions of known NADH concentration verified the performance in terms of reliability and analyte recovery. We herewith established the use of allosteric enzyme modulation and redox polymer-based enzyme electrode wiring for substrate biosensing, a concept that may be applicable to other allosteric enzymes.
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Affiliation(s)
- Somjai Teanphonkrang
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Salome Janke
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry , Chulalongkorn University , 10330 Bangkok , Thailand
| | - Wipa Suginta
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand.,Center of Excellence (CoE) in Advanced Functional Materials, Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Panida Khunkaewla
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Wolfgang Schuhmann
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Adrian Ruff
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
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3
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Roger M, Sciara G, Biaso F, Lojou E, Wang X, Bauzan M, Giudici-Orticoni MT, Vila AJ, Ilbert M. Impact of copper ligand mutations on a cupredoxin with a green copper center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:351-359. [DOI: 10.1016/j.bbabio.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
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4
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Abstract
Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O2-reactive enzymes, raising the possibility that they play an antioxidant protective role. In blue copper proteins with plastocyanin-like domains, Tyr/Trp clusters are uncommon in the low-potential single-domain electron-transfer proteins and in the two-domain copper nitrite reductases. The two-domain muticopper oxidases, however, exhibit clusters of Tyr and Trp residues near the trinuclear copper active site where O2 is reduced. These clusters may play a protective role to ensure that reactive oxygen species are not liberated during O2 reduction.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
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5
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Berry SM, Strange JN, Bladholm EL, Khatiwada B, Hedstrom CG, Sauer AM. Nitrite Reductase Activity in Engineered Azurin Variants. Inorg Chem 2016; 55:4233-47. [PMID: 27055058 DOI: 10.1021/acs.inorgchem.5b03006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrite reductase (NiR) activity was examined in a series of dicopper P.a. azurin variants in which a surface binding copper site was added through site-directed mutagenesis. Four variants were synthesized with copper binding motifs inspired by the catalytic type 2 copper binding sites found in the native noncoupled dinuclear copper enzymes nitrite reductase and peptidylglycine α-hydroxylating monooxygenase. The four azurin variants, denoted Az-NiR, Az-NiR3His, Az-PHM, and Az-PHM3His, maintained the azurin electron transfer copper center, with the second designed copper site located over 13 Å away and consisting of mutations Asn10His,Gln14Asp,Asn16His-azurin, Asn10His,Gln14His,Asn16His-azurin, Gln8Met,Gln14His,Asn16His-azurin, and Gln8His,Gln14His,Asn16His-azurin, respectively. UV-visible absorption spectroscopy, EPR spectroscopy, and electrochemistry of the sites demonstrate copper binding as well as interaction with small exogenous ligands. The nitrite reduction activity of the variants was determined, including the catalytic Michaelis-Menten parameters. The variants showed activity (0.34-0.59 min(-1)) that was slower than that of native NiRs but comparable to that of other model systems. There were small variations in activity of the four variants that correlated with the number of histidines in the added copper site. Catalysis was found to be reversible, with nitrite produced from NO. Reactions starting with reduced azurin variants demonstrated that electrons from both copper centers were used to reduce nitrite, although steady-state catalysis required the T2 copper center and did not require the T1 center. Finally, experiments separating rates of enzyme reduction from rates of reoxidation by nitrite demonstrated that the reaction with nitrite was rate limiting during catalysis.
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Affiliation(s)
- Steven M Berry
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Jacob N Strange
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Erika L Bladholm
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Balabhadra Khatiwada
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Christine G Hedstrom
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Alexandra M Sauer
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
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6
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Hadt RG, Gorelsky S, Solomon EI. Anisotropic covalency contributions to superexchange pathways in type one copper active sites. J Am Chem Soc 2014; 136:15034-45. [PMID: 25310460 PMCID: PMC4210080 DOI: 10.1021/ja508361h] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 01/29/2023]
Abstract
Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu-S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (H(DA)) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu-S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites.
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Affiliation(s)
- Ryan G. Hadt
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Serge
I. Gorelsky
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Centre
for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N6, Canada
| | - Edward I. Solomon
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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MacPherson IS, Rosell FI, Scofield M, Mauk AG, Murphy ME. Directed evolution of copper nitrite reductase to a chromogenic reductant. Protein Eng Des Sel 2010; 23:137-45. [PMID: 20083495 PMCID: PMC2816606 DOI: 10.1093/protein/gzp084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 12/01/2009] [Accepted: 12/09/2009] [Indexed: 11/14/2022] Open
Abstract
Directed evolution methods were developed for Cu-containing nitrite reductase (NiR) from Alcaligenes faecalis S-6. The PCR cloning strategy allows for the efficient production of libraries of 100 000 clones by a modification of a megaprimer-based whole-plasmid synthesis reaction. The high-throughput screen includes colony lift onto a nylon membrane and subsequent lysis of NiR-expressing colonies in the presence of Cu(2+) ions for copper incorporation into intracellularly expressed NiR. Addition of a chromogenic substrate, 3, 3'-diaminobenzidine (DAB), results in deposition of red, insoluble color at the site of oxidation by functional NiR. Twenty-thousand random variants of NiR were screened for improved function with DAB as a reductant, and five variants were identified. These variants were shuffled and screened, yielding two double variants. An analog of the DAB substrate, o-dianisidine, which is oxidized to a water-soluble product was used for functional characterization. The double variant M150L/F312C was most proficient at o-dianisidine oxidation with dioxygen as the electron acceptor (5.5X wt), and the M150L single variant was most proficient at o-dianisidine oxidation with nitrite as the electron acceptor (8.5X wt). The library generation and screening method can be employed for evolving new reductase functions in NiR and for screening of efficient folding of engineered NiRs.
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Affiliation(s)
- Iain S. MacPherson
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- Present address: Department of Biology, Brandeis University, 415 South St, Waltham, MA 02453, USA
| | - Federico I. Rosell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - A. Grant Mauk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michael E.P. Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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8
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Tocheva EI, Rosell FI, Mauk AG, Murphy MEP. Stable Copper−Nitrosyl Formation by Nitrite Reductase in Either Oxidation State. Biochemistry 2007; 46:12366-74. [DOI: 10.1021/bi701205j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elitza I. Tocheva
- Department of Microbiology and Immunology and Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - Federico I. Rosell
- Department of Microbiology and Immunology and Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - A. Grant Mauk
- Department of Microbiology and Immunology and Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Department of Microbiology and Immunology and Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
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9
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Wijma HJ, Jeuken LJC, Verbeet MP, Armstrong FA, Canters GW. Protein film voltammetry of copper-containing nitrite reductase reveals reversible inactivation. J Am Chem Soc 2007; 129:8557-65. [PMID: 17579406 DOI: 10.1021/ja071274q] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cu-containing nitrite reductase from Alcaligenes faecalis S-6 catalyzes the one-electron reduction of nitrite to nitric oxide (NO). Electrons enter the enzyme at the so-called type-1 Cu site and are then transferred internally to the catalytic type-2 Cu site. Protein film voltammetry experiments were carried out to obtain detailed information about the catalytic cycle. The homotrimeric structure of the enzyme is reflected in a distribution of the heterogeneous electron-transfer rates around three main values. Otherwise, the properties and the mode of operation of the enzyme when it is adsorbed as a film on a pyrolytic graphite electrode are essentially unchanged compared to those of the free enzyme in solution. It was established that the reduced type-2 site exists in either an active or an inactive conformation with an interconversion rate of approximately 0.1 s(-1). The random sequential mechanism comprises two routes, one in which the type-2 site is reduced first and subsequently binds nitrite, which is then converted into NO, and another in which the oxidized type-2 site binds nitrite and then accepts an electron to produce NO. At high nitrite concentration, the second route prevails and internal electron transfer is rate-limiting. The midpoint potentials of both sites could be established under catalytic conditions. Binding of nitrite to the type-2 site does not affect the midpoint potential of the type-1 site, thereby excluding cooperativity between the two sites.
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Affiliation(s)
- Hein J Wijma
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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Wijma HJ, MacPherson I, Farver O, Tocheva EI, Pecht I, Verbeet MP, Murphy MEP, Canters GW. Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase. J Am Chem Soc 2007; 129:519-25. [PMID: 17227014 DOI: 10.1021/ja064763j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper-containing nitrite reductase harbors a type-1 and a type-2 Cu site. The former acts as the electron acceptor site of the enzyme, and the latter is the site of catalytic action. The effect of the methionine ligand on the reorganization energy of the type-1 site was explored by studying the electron-transfer kinetics between NiR (wild type (wt) and the variants Met150Gly and Met150Thr) with Fe(II)EDTA and Fe(II)HEDTA. The mutations increased the reorganization energy by 0.3 eV (30 kJ mol-1). A similar increase was found from pulse radiolysis experiments on the wt NIR and three variants (Met150Gly, Met150His, and Met150Thr). Binding of the nearby Met62 to the type-1 Cu site in Met150Gly (under influence of an allosteric effector) lowered the reorganization energy back to approximately the wt value. According to XRD data the structure of the reduced type-1 site in Met150Gly NiR in the presence of an allosteric effector is similar to that in the reduced wt NiR (solved to 1.85 A), compatible with the similarity in reorganization energy.
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Affiliation(s)
- Hein J Wijma
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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