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Fukuda Y, Lintuluoto M, Kurihara K, Hasegawa K, Inoue T, Tamada T. Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography. Biochemistry 2024; 63:339-347. [PMID: 38232298 DOI: 10.1021/acs.biochem.3c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.
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Affiliation(s)
- Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Osaka, Japan
| | - Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai 319-1106, Ibaraki, Japan
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Hyogo, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Chiba, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba 263-8552, Chiba, Japan
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2
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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3
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Szuster J, Zitare UA, Castro MA, Leguto AJ, Morgada MN, Vila AJ, Murgida DH. Cu A-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential. Chem Sci 2020; 11:6193-6201. [PMID: 32953013 PMCID: PMC7480511 DOI: 10.1039/d0sc01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/01/2020] [Indexed: 01/19/2023] Open
Abstract
Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.
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Affiliation(s)
- Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - María A Castro
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
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Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
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Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
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Chen H, Su B, Zhang T, Huang A, Liu H, Yu Y, Wang J. Engineering the metal-binding loop at a type 1 copper center by circular permutation. RSC Adv 2017. [DOI: 10.1039/c7ra11512a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Circular permutation of the cupredoxin azurin creates a break on the metal binding loop, highlighting the loop's flexibility.
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Affiliation(s)
- Honghui Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Binbin Su
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Tongtong Zhang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Haiping Liu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing
- China
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7
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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8
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Abriata LA, Vila AJ, Dal Peraro M. Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control. J Biol Inorg Chem 2014; 19:565-75. [PMID: 24477946 DOI: 10.1007/s00775-014-1108-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a distinct electronic structure compared with those of non-ET-competent copper complexes. The entatic or rack-induced state hypothesis explains these special properties in terms of the strain that the protein matrix exerts on the metal ions. This idea is supported by X-ray structures of apocupredoxins displaying "closed" arrangements of the copper ligands like those observed in the holoproteins; however, it implies completely buried copper-binding atoms, conflicting with the notion that they must be exposed for copper loading. On the other hand, a recent work based on NMR showed that the copper-binding regions of apocupredoxins are flexible in solution. We have explored five cupredoxins in their "closed" apo forms through molecular dynamics simulations. We observed that prearranged ligand conformations are not stable as the X-ray data suggest, although they do form part of the dynamic landscape of the apoproteins. This translates into variable flexibility of the copper-binding regions within a rigid fold, accompanied by fluctuations of the hydrogen bonds around the copper ligands. Major conformations with solvent-exposed copper-binding atoms could allow initial binding of the copper ions. An eventual subsequent incursion to the closed state would result in binding of the remaining ligands, trapping the closed conformation thanks to the additional binding energy and the fastening of noncovalent interactions that make up the rack.
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Affiliation(s)
- Luciano A Abriata
- Laboratory of Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland,
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10
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Allen S, Badarau A, Dennison C. The influence of protein folding on the copper affinities of trafficking and target sites. Dalton Trans 2012; 42:3233-9. [PMID: 23169585 DOI: 10.1039/c2dt32166a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The relative influence of protein unfolding on the Cu(I) affinity of trafficking and target sites for copper has been determined. For the copper metallochaperone Atx1 from Synechocystis PCC 6803 (a cyanobacterium), Saccharomyces cerevisiae and humans unfolding in urea results in a decrease in the Cu(I) affinity from (4-5) × 10(17) M(-1) to (1-3) × 10(16) M(-1) at pH 7. The affinities of the unfolded Atx1s are similar to those for CXXC-containing peptides. Partial unfolding, due to the loop 5 His61Lys mutation in Synechocystis Atx1, gives rise to a more limited decrease in Cu(I) affinity. For the copper target protein plastocyanin from Synechocystis, chemical unfolding results in the Cu(I) affinity decreasing by 5-orders of magnitude. This differential influence of protein unfolding on Cu(I) affinity is due to a more complex copper site structure in the target protein, including numerous interactions of non-coordinating residues with ligating amino acids. This second-coordination sphere is much simpler in the Atx1s with the main interaction provided by the loop 5 residue that tunes the Cu(I) affinity by altering the pK(a) of the C-terminal Cys ligand of the CXXC motif. This interaction and others are absent in the unfolded Atx1s and the two Cys ligands have pK(a) values reminiscent of free thiols (>8) resulting in lowered Cu(I) affinities at pH 7. Residues close to the active site of the thiol-disulfide oxidoreductase thioredoxin appear to lower the Cu(I) affinity of its CXXC motif to 3.1 × 10(15) M(-1) at pH 7, presumably to prevent copper binding in vivo. The structure of a copper site, including the number and relative position of ligands in the primary structure and the complexity of the second-coordination sphere, results in dramatically different effects of unfolding on Cu(I) affinity that has important implications for copper homeostasis.
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Affiliation(s)
- Stephen Allen
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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11
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Monari S, Battistuzzi G, Bortolotti CA, Yanagisawa S, Sato K, Li C, Salard I, Kostrz D, Borsari M, Ranieri A, Dennison C, Sola M. Understanding the Mechanism of Short-Range Electron Transfer Using an Immobilized Cupredoxin. J Am Chem Soc 2012; 134:11848-51. [DOI: 10.1021/ja303425b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Carlo A. Bortolotti
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Sachiko Yanagisawa
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Katsuko Sato
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Chan Li
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Isabelle Salard
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Dorota Kostrz
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Borsari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Antonio Ranieri
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Christopher Dennison
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Sola
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
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12
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Guzzi R, Sportelli L, Yanagisawa S, Li C, Kostrz D, Dennison C. The influence of active site loop mutations on the thermal stability of azurin from Pseudomonas aeruginosa. Arch Biochem Biophys 2012; 521:18-23. [PMID: 22446157 DOI: 10.1016/j.abb.2012.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
Abstract
The copper site and overall structures of azurin (AZ) variants in which the amicyanin (AMI) and plastocyanin (PC) metal binding loops have been introduced, AZAMI and AZPC, respectively, are similar to that of AZ, whereas the loop conformations resemble those in the native proteins. To assess the influence of these loop mutations on stability, the thermal unfolding of AZAMI and AZPC has been investigated by differential scanning calorimetry, absorption and fluorescence spectroscopy. The calorimetric profiles of both variants exhibit a complex shape consisting of two endothermic peaks and an exothermic peak. The temperature of the maximum heat of absorption for the single endothermic peak is 82.7°C for AZ, whereas for AZAMI and AZPC the most intense endothermic peaks are at 74.9 and 68.1°C comparable to values for AMI and PC, respectively. Denaturation investigated using the temperature dependence of the absorbance at ∼600nm and Trp emission, also demonstrates decreased stability for both loop mutants. The thermal transition between the native and the denaturated states is irreversible, scan rate dependent and consistent with the two-state irreversible model. The structure of the active-site loop has a dramatic effect on the kinetic stability and the unfolding pathway of cupredoxins.
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Affiliation(s)
- Rita Guzzi
- Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, Ponte P. Bucci, Cubo 31C, 87036 Rende (CS), Italy.
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13
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Incorporation of the red copper nitrosocyanin binding loop into blue copper azurin. J Biol Inorg Chem 2010; 16:473-80. [DOI: 10.1007/s00775-010-0746-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
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14
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Li C, Sato K, Monari S, Salard I, Sola M, Banfield MJ, Dennison C. Metal-Binding Loop Length Is a Determinant of the pKa of a Histidine Ligand at a Type 1 Copper Site. Inorg Chem 2010; 50:482-8. [DOI: 10.1021/ic101413e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katsuko Sato
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Isabelle Salard
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Marco Sola
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, U.K
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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15
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Su P, Li H. Protonation of Type-1 Cu Bound Histidines: A Quantum Chemical Study. Inorg Chem 2009; 49:435-44. [DOI: 10.1021/ic9012735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peifeng Su
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Hui Li
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
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Abstract
The C-terminal copper-binding loop in the beta-barrel fold of the cupredoxin azurin has been replaced with a range of sequences containing alanine, glycine, and valine residues to assess the importance of amino acid composition and the length of this region. The introduction of 2 and 4 alanines between the coordinating Cys, His, and Met results in loop structures matching those in naturally occurring proteins with the same loop lengths. A loop with 4 alanines between the Cys and His and 3 between the His and Met ligands has a structure identical to that of the WT protein, whose loop is the same length. Loop structure is dictated by length and not sequence allowing the properties of the main surface patch for interactions with partners, to which the loop is a major contributor, to be optimized. Loops with 2 amino acids between the ligands using glycine, alanine, and valine residues have been compared. An empirical relationship is found between copper site protection by the loop and reduction potential. A loop adorned with 4 methyl groups is sufficient to protect the copper ion, enabling most sequences to adequately perform this task. The mutant with 3 alanine residues between the ligands forms a strand-swapped dimer in the crystal structure, an arrangement that has not, to our knowledge, been seen previously for this family of proteins. Cupredoxins function as redox shuttles and are required to be monomeric; therefore, none have evolved with a metal-binding loop of this length.
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Active site loop dictates the thermodynamics of reduction and ligand protonation in cupredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:995-1000. [PMID: 19230853 DOI: 10.1016/j.bbapap.2009.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 11/21/2022]
Abstract
The thermodynamics of reduction and His ligand protonation have been determined for a range of loop-contraction variants of the electron transferring type 1 copper protein azurin (AZ). For AZPC, in which the native C-terminal loop containing the Cys, His and Met ligands has been replaced with the shorter sequence from plastocyanin (PC) and AZAMI, in which the even shorter amicyanin (AMI) loop has been inserted, the thermodynamics of reduction match those of the protein whose loop has been introduced which are different to the values for AZ. The enthalpic contribution to His ligand protonation, which is not observed in AZ, is similar in AZAMI and AMI. The thermodynamics of this process in AZPC are more dissimilar to those for PC. In the case of AZAMI-F, a variant possessing the (non natural) minimal loop that can bind a type 1 copper site, the reduction thermodynamics are intermediate between those of AZPC and AZAMI, whilst the thermodynamic data for His ligand protonation are very similar to those for AMI. The results for AZAMI and AZPC are primarily due to protein based enthalpic effects related to the interaction of the metal with permanent protein dipoles from the loop, and to the decreased loop length which favors His ligand protonation in the cuprous proteins. Entropic factors related to loop flexibility have little influence because of constraints imposed by metal coordination and the fact that the introduced loops pack well against the AZ scaffold. Thus, the host scaffold in general plays a minor thermodynamic role in both processes, although for AZAMI-F differences in the first and second coordination spheres influence the thermodynamics of reduction.
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Yanagisawa S, Crowley PB, Firbank SJ, Lawler AT, Hunter DM, McFarlane W, Li C, Kohzuma T, Banfield MJ, Dennison C. π-Interaction Tuning of the Active Site Properties of Metalloproteins. J Am Chem Soc 2008; 130:15420-8. [DOI: 10.1021/ja8038135] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Peter B. Crowley
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Susan J. Firbank
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Anne T. Lawler
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - David M. Hunter
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - William McFarlane
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Takamitsu Kohzuma
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Mark J. Banfield
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
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Sato K, Firbank S, Li C, Banfield M, Dennison C. The Importance of the Long Type 1 Copper‐Binding Loop of Nitrite Reductase for Structure and Function. Chemistry 2008; 14:5820-8. [DOI: 10.1002/chem.200701997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Abstract
Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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21
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Harris KL, Lim S, Franklin SJ. Of Folding and Function: Understanding Active-Site Context through Metalloenzyme Design. Inorg Chem 2006; 45:10002-12. [PMID: 17140195 DOI: 10.1021/ic060877k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the emerging field of biomolecular design, the introduction of metal-binding sites into loop or turn regions of known protein scaffolds has been utilized to create unique metalloprotein and metallopeptide systems for study. This Forum Article highlights examples of the modular-turn-substitution approach to design and the range of structural and mechanistic questions to which this tool can be applied. Examples from the authors' laboratory are given to show that lanthanide-binding metallopeptides, and now a full metallohomeodomain, can be generated by modular substitution of a Ca-binding EF-hand loop into the unrelated scaffold, the engrailed helix-turn-helix motif. We have previously shown that these peptides bind trivalent Ln(III) ions and promote DNA and phosphate hydrolysis, the targeted function. Here, a series of chimeric peptides are presented that differ only in the ninth loop position [given in parentheses; Peptides P3N (Asn), P3E (Glu), P3A (Ala), and P3W(D) (Asp]. This residue, a putative second-shell ligand stabilizing a coordinated water, was found to influence not only metal affinity but also peptide folding. The affinity for Tb(III) was determined by Trp-Tb fluorescence resonance energy transfer and followed the order Ka = P3W(D) > P3A approximately P3E > P3N. However, circular dichroism (CD) titrations with EuCl3 showed that only P3W(D) and P3N folded to any extent upon metal binding, indicating that the Asp/Asn side chains stabilize the central loop structure and thus propagate folding of the peripheral helices, whereas neither Ala nor Glu appears to be interacting with the metal to organize the loop. Finally, we investigated the longer range context of a given loop substitution by cloning and expressing a lanthanide-binding homeodomain (C2), whose loop insertion sequence is analogous to that of peptide P3W(D). We find by CD that apo-C2 has a significant helical structure (approximately 25% alphahelicity), which increases further upon the addition of Tb(III) (approximately 32% alpha helicity). The protein's Tb(III) affinity is similar to that of the chimeric peptides. However, unlike previously reported metallopeptides, we find that EuC2 does not appreciably promote phosphate or DNA cleavage, which suggests a difference in metal accessibility in the context of the full domain. We have demonstrated that substituting beta turns with metal-binding turns does not necessarily require homologous parental scaffolds or small flexible peptides but rather relies on the structural similarity of the motifs flanking the turn.
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Affiliation(s)
- Kinesha L Harris
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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22
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Li C, Yanagisawa S, Martins BM, Messerschmidt A, Banfield MJ, Dennison C. Basic requirements for a metal-binding site in a protein: the influence of loop shortening on the cupredoxin azurin. Proc Natl Acad Sci U S A 2006; 103:7258-63. [PMID: 16651527 PMCID: PMC1464330 DOI: 10.1073/pnas.0600774103] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Indexed: 11/18/2022] Open
Abstract
The main active-site loop of the copper-binding protein azurin (a cupredoxin) has been shortened from C(112)TFPGH(117)SALM(121) to C(112)TPH(115)PFM(118) (the native loop from the cupredoxin amicyanin) and also to C(112)TPH(115)PM(117). The Cu(II) site structure is almost unaffected by shortening, as is that of the Cu(I) center at alkaline pH in the variant with the C(112)TPH(115)PM(117) loop sequence. Subtle spectroscopic differences due to alterations in the spin density distribution at the Cu(II) site can be attributed mainly to changes in the hydrogen-bonding pattern. Electron transfer is almost unaffected by the introduction of the C(112)TPH(115)PFM(118) loop, but removal of the Phe residue has a sizable effect on reactivity, probably because of diminished homodimer formation. At mildly acidic pH values, the His-115 ligand protonates and dissociates from the cuprous ion, an effect that has a dramatic influence on the reactivity of cupredoxins. These studies demonstrate that the amicyanin loop adopts a conformation identical to that found in the native protein when introduced into azurin, that a shorter than naturally occurring C-terminal active-site loop can support a functional T1 copper site, that CTPHPM is the minimal loop length required for binding this ubiquitous electron transfer center, and that the length and sequence of a metal-binding loop regulates a range of structural and functional features of the active site of a metalloprotein.
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Affiliation(s)
- Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Berta M. Martins
- Elitenetzwerk Bayern Macromolecular Science, Mikrobiologie/Proteinkristallographie Laboratories, Universität Bayreuth, D-95440 Bayreuth, Germany; and
| | - Albrecht Messerschmidt
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mark J. Banfield
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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24
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Dennison C. Ligand and loop variations at type 1 copper sites: influence on structure and reactivity. Dalton Trans 2005:3436-42. [PMID: 16234922 DOI: 10.1039/b507440c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK NE2 4HH.
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