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Bonczidai-Kelemen D, Tóth K, Fábián I, Lihi N. The role of the terminal cysteine moiety in a metallopeptide mimicking the active site of the NiSOD enzyme. Dalton Trans 2024; 53:1648-1656. [PMID: 38168682 DOI: 10.1039/d3dt03638c] [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: 01/05/2024]
Abstract
Superoxide dismutase (SOD) enzymes are pivotal in regulating oxidative stress. In order to model Ni containing SOD enzymes, the results of the thermodynamic, spectroscopic and SOD activity studies on the complexes formed between nickel(II) and a NiSOD related peptide, CysCysAspLeuProCysGlyValTyr-NH2 (wtCC), are reported. Cysteine was introduced to replace the first histidine residue in the amino acid sequence of the active site of the NiSOD enzyme. The novel peptide exhibits 3 times higher metal binding affinity compared to the native NiSOD fragment. This is due to the presence of the first cysteine in the coordination sphere of nickel(II). At physiological pH, the (NH2,S-,S-,S-) coordinated complex is the major species. This coordination mode is altered when one thiolate group is replaced by an amide nitrogen of the peptide backbone above pH 7.5. The nickel complexes of wtCC exhibit similar SOD activity to that of the complex formed with the active site fragment of the native NiSOD. The reaction between the complexes and the superoxide anion was studied by the sequential stopped-flow method. These studies revealed that the nickel(II) complex is always in excess over the nickel(III) complex during the dismutation process. However, the nickel(III) species is also involved in a relatively fast degradation process. This unambiguously proves that a protective mechanism must be operative in the NiSOD enzyme which prevents the oxidation of the sulfur atom of cysteine in the presence of O2-. The results provide new possibilities for the use of NiSOD mimics in bio- and industrial catalytic processes.
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Affiliation(s)
- Dóra Bonczidai-Kelemen
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
- Doctoral School of Chemistry, University of Debrecen, Debrecen H-4032, Hungary
| | - Klaudia Tóth
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - István Fábián
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Norbert Lihi
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
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Basak P, Cabelli DE, Chivers PT, Farquhar ER, Maroney MJ. In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation. Metallomics 2023; 15:mfad054. [PMID: 37723610 PMCID: PMC10628968 DOI: 10.1093/mtomcs/mfad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
The importance of cellular low molecular weight ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of nickel-dependent superoxide dismutase (NiSOD) from Streptomyces coelicolor. In vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.
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Affiliation(s)
- Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Diane E Cabelli
- Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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Domergue J, Guinard P, Douillard M, Pécaut J, Hostachy S, Proux O, Lebrun C, Le Goff A, Maldivi P, Duboc C, Delangle P. A Series of Ni Complexes Based on a Versatile ATCUN-Like Tripeptide Scaffold to Decipher Key Parameters for Superoxide Dismutase Activity. Inorg Chem 2023. [PMID: 37247425 DOI: 10.1021/acs.inorgchem.3c00766] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The cellular level of reactive oxygen species (ROS) has to be controlled to avoid some pathologies, especially those linked to oxidative stress. One strategy for designing antioxidants consists of modeling natural enzymes involved in ROS degradation. Among them, nickel superoxide dismutase (NiSOD) catalyzes the dismutation of the superoxide radical anion, O2•-, into O2 and H2O2. We report here Ni complexes with tripeptides derived from the amino-terminal CuII- and NiII-binding (ATCUN) motif that mimics some structural features found in the active site of the NiSOD. A series of six mononuclear NiII complexes were investigated in water at physiological pH with different first coordination spheres, from compounds with a N3S to N2S2 set, and also complexes that are in equilibrium between the N-coordination (N3S) and S-coordination (N2S2). They were fully characterized by a combination of spectroscopic techniques, including 1H NMR, UV-vis, circular dichroism, and X-ray absorption spectroscopy, together with theoretical calculations and their redox properties studied by cyclic voltammetry. They all display SOD-like activity, with a kcat ranging between 0.5 and 2.0 × 106 M-1 s-1. The complexes in which the two coordination modes are in equilibrium are the most efficient, suggesting a beneficial effect of a nearby proton relay.
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Affiliation(s)
- Jérémy Domergue
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Pawel Guinard
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Magali Douillard
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Jacques Pécaut
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Sarah Hostachy
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Olivier Proux
- CNRS, OSUG, Université Grenoble Alpes, 38000 Grenoble, France
| | - Colette Lebrun
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Alan Le Goff
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
| | - Pascale Maldivi
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
| | - Pascale Delangle
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
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Basak P, Zambelli B, Cabelli DE, Ciurli S, Maroney MJ. Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase. J Inorg Biochem 2022; 234:111858. [DOI: 10.1016/j.jinorgbio.2022.111858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/30/2022] [Accepted: 05/07/2022] [Indexed: 01/23/2023]
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Alfano M, Cavazza C. Structure, function, and biosynthesis of nickel-dependent enzymes. Protein Sci 2020; 29:1071-1089. [PMID: 32022353 DOI: 10.1002/pro.3836] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
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Affiliation(s)
- Marila Alfano
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
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Alfano M, Veronesi G, Musiani F, Zambelli B, Signor L, Proux O, Rovezzi M, Ciurli S, Cavazza C. A Solvent‐Exposed Cysteine Forms a Peculiar Ni
II
‐Binding Site in the Metallochaperone CooT from
Rhodospirillum rubrum. Chemistry 2019; 25:15351-15360. [DOI: 10.1002/chem.201903492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Marila Alfano
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Giulia Veronesi
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Francesco Musiani
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Luca Signor
- IRIG, IBSUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Olivier Proux
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Mauro Rovezzi
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Christine Cavazza
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
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Domergue J, Pécaut J, Proux O, Lebrun C, Gateau C, Le Goff A, Maldivi P, Duboc C, Delangle P. Mononuclear Ni(II) Complexes with a S3O Coordination Sphere Based on a Tripodal Cysteine-Rich Ligand: pH Tuning of the Superoxide Dismutase Activity. Inorg Chem 2019; 58:12775-12785. [PMID: 31545024 DOI: 10.1021/acs.inorgchem.9b01686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The superoxide dismutase (SOD) activity of mononuclear NiII complexes, whose structures are inspired by the NiSOD, has been investigated. They have been designed with a sulfur-rich pseudopeptide ligand, derived from nitrilotriacetic acid (NTA), where the three acid functions are grafted with cysteines (L3S). Two mononuclear complexes, which exist in pH-dependent proportions, have been fully characterized by a combination of spectroscopic techniques including 1H NMR, UV-vis, circular dichroism, and X-ray absorption spectroscopy, together with theoretical calculations. They display similar square-planar S3O coordination, with the three thiolates of the three cysteine moieties from L3S coordinated to the NiII ion, together with either a water molecule at physiological pH, as [NiL3S(OH2)]-, or a hydroxo ion in more basic conditions, as [NiL3S(OH)]2-. The 1H NMR study has revealed that contrary to the hydroxo ligand, the bound water molecule is labile. The cyclic voltammogram of both complexes displays an irreversible one-electron oxidation process assigned to the NiII/NiIII redox system with Epa = 0.48 and 0.31 V versus SCE for NiL3S(OH2) and NiL3S(OH), respectively. The SOD activity of both complexes has been tested. On the basis of the xanthine oxidase assay, an IC50 of about 1 μM has been measured at pH 7.4, where NiL3S(OH2) is mainly present (93% of the NiII species), while the IC50 is larger than 100 μM at pH 9.6, where NiL3S(OH) is the major species (92% of the NiII species). Interestingly, only NiL3S(OH2) displays SOD activity, suggesting that the presence of a labile ligand is required. The SOD activity has been also evaluated under catalytic conditions at pH 7.75, where the ratio between NiL3S(OH2)/ NiL3S(OH) is about (86:14), and a rate constant, kcat = 1.8 × 105 M-1 s-1, has been measured. NiL3S(OH2) is thus the first low-molecular weight, synthetic, bioinspired Ni complex that displays catalytic SOD activity in water at physiological pH, although it does not contain any N-donor ligand in its first coordination sphere, as in the NiSOD. Overall, the data show that a key structural feature is the presence of a labile ligand in the coordination sphere of the NiII ion.
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Affiliation(s)
- Jérémy Domergue
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France.,Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Jacques Pécaut
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Olivier Proux
- Univ. Grenoble Alpes, CNRS, OSUG , 38000 Grenoble , France
| | - Colette Lebrun
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Christelle Gateau
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Alan Le Goff
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - Pascale Maldivi
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
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