1
|
Kekez I, Faletar M, Kekez M, Cendron L, Wright M, Zanotti G, Matković-Čalogović D. Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori. Molecules 2022; 27:molecules27113387. [PMID: 35684325 PMCID: PMC9182242 DOI: 10.3390/molecules27113387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.
Collapse
Affiliation(s)
- Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
- Correspondence: (I.K.); (D.M.-Č.); Tel.: +385-14-606-345 (D.M.-Č.)
| | - Mihovil Faletar
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
| | - Mario Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
| | - Laura Cendron
- Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Maya Wright
- Fluidic Analytics Ltd., Unit A Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK;
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Dubravka Matković-Čalogović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
- Correspondence: (I.K.); (D.M.-Č.); Tel.: +385-14-606-345 (D.M.-Č.)
| |
Collapse
|
2
|
Hadley RC, Zhitnitsky D, Livnat-Levanon N, Masrati G, Vigonsky E, Rose J, Ben-Tal N, Rosenzweig AC, Lewinson O. The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery. J Biol Chem 2022; 298:101445. [PMID: 34822841 PMCID: PMC8689200 DOI: 10.1016/j.jbc.2021.101445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
The Escherichia coli yobA-yebZ-yebY (AZY) operon encodes the proteins YobA, YebZ, and YebY. YobA and YebZ are homologs of the CopC periplasmic copper-binding protein and the CopD putative copper importer, respectively, whereas YebY belongs to the uncharacterized Domain of Unknown Function 2511 family. Despite numerous studies of E. coli copper homeostasis and the existence of the AZY operon in a range of bacteria, the operon's proteins and their functional roles have not been explored. In this study, we present the first biochemical and functional studies of the AZY proteins. Biochemical characterization and structural modeling indicate that YobA binds a single Cu2+ ion with high affinity. Bioinformatics analysis shows that YebY is widespread and encoded either in AZY operons or in other genetic contexts unrelated to copper homeostasis. We also determined the 1.8 Å resolution crystal structure of E. coli YebY, which closely resembles that of the lantibiotic self-resistance protein MlbQ. Two strictly conserved cysteine residues form a disulfide bond, consistent with the observed periplasmic localization of YebY. Upon treatment with reductants, YebY binds Cu+ and Cu2+ with low affinity, as demonstrated by metal-binding analysis and tryptophan fluorescence. Finally, genetic manipulations show that the AZY operon is not involved in copper tolerance or antioxidant defense. Instead, YebY and YobA are required for the activity of the copper-related NADH dehydrogenase II. These results are consistent with a potential role of the AZY operon in copper delivery to membrane proteins.
Collapse
Affiliation(s)
- Rose C Hadley
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Daniel Zhitnitsky
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Nurit Livnat-Levanon
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elena Vigonsky
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Jessica Rose
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Oded Lewinson
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
3
|
Ipsen JØ, Hernández-Rollán C, Muderspach SJ, Brander S, Bertelsen AB, Jensen PE, Nørholm MHH, Lo Leggio L, Johansen KS. Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC. FEBS Lett 2021; 595:1708-1720. [PMID: 33896006 DOI: 10.1002/1873-3468.14092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/11/2022]
Abstract
The histidine brace (His-brace) is a copper-binding motif that is associated with both oxidative enzymes and proteinaceous copper chaperones. Here, we used biochemical and structural methods to characterize mutants of a His-brace-containing copper chaperone from Pseudomonas fluorescens (PfCopC). A total of 15 amino acid variants in primary and second-sphere residues were produced and characterized in terms of their copper binding and redox properties. PfCopC has a very high affinity for Cu(II) and also binds Cu(I). A high reorganization barrier likely prevents redox cycling and, thus, catalysis. In contrast, mutations in the conserved second-sphere Glu27 enable slow oxidation of ascorbate. The crystal structure of the variant E27A confirmed copper binding at the His-brace. Unexpectedly, Asp83 at the equatorial position was shown to be indispensable for Cu(II) binding in the His-brace of PfCopC. A PfCopC mutant that was designed to mimic the His-brace from lytic polysaccharide monooxygenase-like family X325 did not bind Cu(II), but was still able to bind Cu(I). These results highlight the importance of the proteinaceous environment around the copper His-brace for reactivity and, thus, the difference between enzyme and chaperone.
Collapse
Affiliation(s)
- Johan Ø Ipsen
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Søren Brander
- Department of Geosciences and Natural Resource Management, Copenhagen University, Frederiksberg, Denmark
| | - Andreas B Bertelsen
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, Copenhagen University, Frederiksberg, Denmark
| |
Collapse
|
4
|
Tikhonova TV, Lilina AV, Osipov EM, Shipkov NS, Dergousova NI, Kulikova OG, Popov VO. Catalytic Properties of Flavocytochrome c Sulfide Dehydrogenase from Haloalkaliphilic Bacterium Thioalkalivibrio paradoxus. BIOCHEMISTRY (MOSCOW) 2021; 86:361-369. [PMID: 33838635 DOI: 10.1134/s0006297921030111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Flavocytochrome c sulfide dehydrogenase (FCC) is one of the central enzymes of the respiratory chain in sulfur-oxidizing bacteria. FCC catalyzes oxidation of sulfide and polysulfide ions to elemental sulfur accompanied by electron transfer to cytochrome c. The catalytically active form of the enzyme is a non-covalently linked heterodimer composed of flavin- and heme-binding subunits. The Thioalkalivibrio paradoxus ARh1 genome contains five copies of genes encoding homologous FCCs with an amino acid sequence identity from 36 to 54%. When growing on thiocyanate or thiosulfate as the main energy source, the bacterium synthesizes products of different copies of FCC genes. In this work, we isolated and characterized FCC synthesized during the growth of Tv. paradoxus on thiocyanate. FCC was shown to oxidize exclusively sulfide but not other reduced sulfur compounds, such as thiosulfate, sulfite, tetrathionate, and sulfur, and it also does not catalyze the reverse reaction of sulfur reduction to sulfide. Kinetic parameters of the sulfide oxidation reaction are characterized.
Collapse
Affiliation(s)
- Tamara V Tikhonova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Anastasiya V Lilina
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Evgenii M Osipov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Nikolay S Shipkov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Nataliya I Dergousova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Olga G Kulikova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| |
Collapse
|
5
|
Brander S, Horvath I, Ipsen JØ, Peciulyte A, Olsson L, Hernández-Rollán C, Nørholm MHH, Mossin S, Leggio LL, Probst C, Thiele DJ, Johansen KS. Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace. Sci Rep 2020; 10:16369. [PMID: 33004835 PMCID: PMC7529816 DOI: 10.1038/s41598-020-73266-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
Collapse
Affiliation(s)
- Søren Brander
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Istvan Horvath
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Johan Ø Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Ausra Peciulyte
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Susanne Mossin
- Centre for Catalysis and Sustainable Chemistry, Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Corinna Probst
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dennis J Thiele
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Katja S Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
| |
Collapse
|
6
|
Trisolini L, Gambacorta N, Gorgoglione R, Montaruli M, Laera L, Colella F, Volpicella M, De Grassi A, Pierri CL. FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function. J Clin Med 2019; 8:jcm8122117. [PMID: 31810296 PMCID: PMC6947548 DOI: 10.3390/jcm8122117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure-function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Anna De Grassi
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| | - Ciro Leonardo Pierri
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| |
Collapse
|
7
|
Udagedara SR, Wijekoon CJ, Xiao Z, Wedd AG, Maher MJ. The crystal structure of the CopC protein from Pseudomonas fluorescens reveals amended classifications for the CopC protein family. J Inorg Biochem 2019; 195:194-200. [DOI: 10.1016/j.jinorgbio.2019.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/26/2019] [Accepted: 03/07/2019] [Indexed: 01/09/2023]
|
8
|
X-Ray Structure of Human Sulfide:Quinone Oxidoreductase: Insights into the Mechanism of Mitochondrial Hydrogen Sulfide Oxidation. Structure 2019; 27:794-805.e4. [PMID: 30905673 DOI: 10.1016/j.str.2019.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Hydrogen sulfide (H2S) is a gasotransmitter exhibiting pivotal functions in diverse biological processes, including activation of multiple cardioprotective pathways. Sulfide:quinone oxidoreductase (SQOR) is an integral membrane flavoprotein that catalyzes the first step in the mitochondrial metabolism of H2S. As such, it plays a critical role in controlling physiological levels of the gasotransmitter and has attracted keen interest as a potential drug target. We report the crystal structure of human SQOR, unraveling the molecular basis for the enzyme's ability to catalyze sulfane sulfur transfer reactions with structurally diverse acceptors. We demonstrate that human SQOR contains unique features: an electropositive surface depression implicated as a binding site for sulfane sulfur acceptors and postulated to funnel negatively charged substrates to a hydrophilic H2S-oxidizing active site, which is connected to a hydrophobic internal tunnel that binds coenzyme Q. These findings support a proposed model for catalysis and open the door for structure-based drug design.
Collapse
|