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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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2
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Guo L, Cheng X, Jiang HY, Dai YJ. Maturation Mechanism of Nitrile Hydratase From Streptomyces canus CGMCC 13662 and Its Structural Character. Front Microbiol 2020; 11:1419. [PMID: 32670250 PMCID: PMC7329996 DOI: 10.3389/fmicb.2020.01419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrile hydratases have received significant interest both in the large-scale industrial production of acrylamide and nicotinamide, and the remediation of environmental contamination with nitrile-containing pollutants. Almost all known nitrile hydratases include an α-subunit (AnhA) and β-subunit (AnhB), and a specific activator protein is crucial for their maturation and catalytic activity. Many studies exist on nitrile hydratase characteristics and applications, but few have reported their metal insertion and post-translational maturation mechanism. In this study, we investigated the cobalt insertion and maturation mechanism of nitrile hydratase from Streptomyces canus CGMCC 13662 (ScNHase) bearing three subunits (AnhD, AnhE, and AnhA). ScNHase subunits were purified, and the cobalt content and nitrile hydratase activity of the ScNHase subunits were detected. We discovered that cobalt could insert into the cobalt-free AnhA of ScNHase in the absence of activator protein under reduction agent DL-dithiothreitol (DTT) environment. AnhD not only performed the function of AnhB of NHase, but also acted as a metal ion chaperone and self-subunit swapping chaperone, while AnhE did not act as similar performance. A cobalt direct-insertion under reduction condition coordinated self-subunit swapping mechanism is responsible for ScNHase post-translational maturation. Molecular docking of ScNHase and substrates suggested that the substrate specificity of ScNHase was correlated with its structure. ScNHase had a weak hydrophobic interaction with IAN through protein-ligand interaction analysis and, therefore, had no affinity with indole-3-acetonitrile (IAN). The post-translational maturation mechanism and structure characteristics of ScNHase could help guide research on the environmental remediation of nitrile-containing waste contamination and three-subunit nitrile hydratase.
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Affiliation(s)
- Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xi Cheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Huo-Yong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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4
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Beheshti A, Mousavifard ES, Noorizadeh S, Mayer P, Woźniak K. Impact of cyanide co-ligand to convert crystal structure of pyrazole-based copper coordination compounds from a dinuclear to a polymeric structure and DFT calculations of [Cu2(tpmp)X2] (X = Cl and I). Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Emergence of metal selectivity and promiscuity in metalloenzymes. J Biol Inorg Chem 2019; 24:517-531. [DOI: 10.1007/s00775-019-01667-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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6
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Xia Y, Peplowski L, Cheng Z, Wang T, Liu Z, Cui W, Kobayashi M, Zhou Z. Metallochaperone function of the self‐subunit swapping chaperone involved in the maturation of subunit‐fused cobalt‐type nitrile hydratase. Biotechnol Bioeng 2019; 116:481-489. [DOI: 10.1002/bit.26865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus UniversityTorun Poland
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Tianyi Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, TennodaiTsukuba Ibaraki Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
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Xia W, Li H, Sun H. Nickel Metallochaperones: Structure, Function, and Nickel-Binding Properties. THE BIOLOGICAL CHEMISTRY OF NICKEL 2017. [DOI: 10.1039/9781788010580-00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nickel-containing enzymes catalyze a series of important biochemical processes in both prokaryotes and eukaryotes. The maturation of the enzymes requires the proper assembly of the nickel-containing active sites, which involves a battery of nickel metallochaperones that exert metal delivery and storage functions. “Cross-talk” also exists between different nickel enzyme maturation processes. This chapter summarizes the updated knowledge about the nickel chaperones based on biochemical and structural biology research, and discusses the possible nickel delivery mechanisms.
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Affiliation(s)
- Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
| | - Hongzhe Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
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8
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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9
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Xia Y, Cui W, Liu Z, Zhou L, Cui Y, Kobayashi M, Zhou Z. Construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern. Sci Rep 2016; 6:19183. [PMID: 26755342 PMCID: PMC4709657 DOI: 10.1038/srep19183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 12/07/2015] [Indexed: 01/10/2023] Open
Abstract
Metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. The metal is usually transferred between different proteins. In this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (NHase). Various “activator proteins” mediate the trafficking of metal ions into NHases. We constructed fusion NHases by fusing the β- and α-subunits and/or the “activator proteins” of the NHase from Pseudomonas putida. The fusion NHases exhibited higher thermostability and tolerance to high concentrations of the product amide. The mechanism of the cobalt incorporation changed from a self-subunit swapping pattern to an apoprotein-specific molecular chaperone pattern in vivo and a metallochaperone pattern in vitro. Notably, the cobalt transfer occurred between the same α-subunit in the metallochaperone pattern. These results not only demonstrated the superiority of fusion-type NHases, but also revealed an innovative metal ion transfer pattern in metalloprotein biosynthesis.
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Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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10
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Denny JA, Foley WS, Todd AD, Darensbourg MY. The ligand unwrapping/rewrapping pathway that exchanges metals in S-acetylated, hexacoordinate N 2S 2O 2 complexes. Chem Sci 2015; 6:7079-7088. [PMID: 29896341 PMCID: PMC5954489 DOI: 10.1039/c5sc02269j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/05/2015] [Indexed: 12/13/2022] Open
Abstract
The effect of S-acetylation in MN2S2 complexes on metal exchange reactivity was examined in a series of MN2S2O2 complexes. While clean exchange processes do not occur for the MN2S2 derivatives where formation of S-bridged aggregates predominate, acetylation permits the metal exchange with hierarchy that follows the Irving-Williams series of stability for first row transition metals: Fe2+ < Co2+ < Ni2+ < Cu2+ > Zn2+. The rate determining step consistent with kinetic parameters depends on both M and M', supporting a mechanism of exchange that involves ligand unwrapping/rewrapping process as earlier defined by Margerum et al. for M(EDTA) systems. The enhanced metal exchange deriving from S-acetylation is of significance to probes and detection of cysteine-S metallo-proteins and metallo-enzyme active sites, and highlights a new role for S-acetylation.
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Affiliation(s)
- J A Denny
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - W S Foley
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - A D Todd
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - M Y Darensbourg
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
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11
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Farrugia MA, Wang B, Feig M, Hausinger RP. Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease. Biochemistry 2015; 54:6392-401. [PMID: 26401965 DOI: 10.1021/acs.biochem.5b00942] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nickel-containing urease from Klebsiella aerogenes requires four accessory proteins for proper active site metalation. The metallochaperone UreE delivers nickel to UreG, a GTPase that forms a UreD/UreF/UreG complex, which binds to urease apoprotein via UreD. Prior in silico analysis of the homologous, structurally characterized UreH/UreF/UreG complex from Helicobacter pylori identified a water tunnel originating at a likely nickel-binding motif in UreG, passing through UreF, and exiting UreH, suggestive of a role for the channel in providing the metal to urease apoprotein for its activation; however, no experimental support was reported for the significance of this tunnel. Here, specific variants were designed to disrupt a comparable 34.6 Å predicted internal tunnel, alternative channels, and surface sites for UreD. Cells producing a set of tunnel-disrupting variants of UreD exhibited greatly reduced urease specific activities, whereas other mutants had no appreciable effect on activity. Affinity pull-down studies of cell-free extracts from tunnel-disrupting mutant cultures showed no loss of UreD interactions with urease or UreF/UreG. The nickel contents of urease samples enriched from activity-deficient cultures were decreased, while zinc and iron incorporation increased. Molecular dynamics simulations revealed size restrictions in the internal channels of the UreD variants. These findings support the role of a molecular tunnel in UreD as a direct facilitator of nickel transfer into urease, illustrating a new paradigm in active site metallocenter assembly.
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Affiliation(s)
- Mark A Farrugia
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Beibei Wang
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
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12
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Advances in microbial biosynthesis of metal nanoparticles. Appl Microbiol Biotechnol 2015; 100:521-34. [PMID: 26300292 DOI: 10.1007/s00253-015-6904-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 01/30/2023]
Abstract
Metal nanoparticles are garnering considerable attention owing to their high potential for use in various applications in the material, electronics, and energy industries. Recent research efforts have focused on the biosynthesis of metal nanomaterials using microorganisms rather than traditional chemical synthesis methods. Microorganisms have evolved to possess molecular machineries for detoxifying heavy metals, mainly by employing metal-binding proteins and peptides. Biosynthesis of diverse metal nanoparticles has recently been demonstrated using such heavy metal detoxification systems in microorganisms, which provides several advantages over the traditional chemical synthesis methods. First, metal nanoparticles can be synthesized at mild temperatures, such as at room temperature, with less energy input. Second, no toxic chemicals or reagents are needed, and thus the process is environmentally friendly. Third, diverse metal nanoparticles, including those that have never been chemically synthesized, can be biosynthesized. Here, we review the strategies for the biosynthesis of metal nanoparticles using microorganisms, and provide future prospects.
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13
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Yu D, Hui Y, Zai X, Xu J, Liang L, Wang B, Yue J, Li S. Comparative genomic analysis of Brucella abortus vaccine strain 104M reveals a set of candidate genes associated with its virulence attenuation. Virulence 2015; 6:745-54. [PMID: 26039674 DOI: 10.1080/21505594.2015.1038015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used as a vaccine strain in humans against brucellosis for 6 decades in China. Despite many studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we determined the whole-genome sequence of 104M and conducted a comprehensive comparative analysis against the whole genome sequences of the virulent strain, A13334, and other reference strains. This analysis revealed a highly similar genome structure between 104M and A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of genes missing in 104M. Some of these genes were identified to be directly or indirectly associated with virulence. Similarly, a set of mutations in the virulence-related genes was also identified, which may be related to virulence alteration. This study provides a set of candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.
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Affiliation(s)
- Dong Yu
- a Beijing Institute of Biotechnology ; Beijing , PR China
| | - Yiming Hui
- b LanZhou Institute of Biological Products ; Lanzhou , PR China
| | - Xiaodong Zai
- a Beijing Institute of Biotechnology ; Beijing , PR China
| | - Junjie Xu
- a Beijing Institute of Biotechnology ; Beijing , PR China
| | - Long Liang
- a Beijing Institute of Biotechnology ; Beijing , PR China
| | - Bingxiang Wang
- b LanZhou Institute of Biological Products ; Lanzhou , PR China
| | - Junjie Yue
- a Beijing Institute of Biotechnology ; Beijing , PR China
| | - Shanhu Li
- a Beijing Institute of Biotechnology ; Beijing , PR China
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14
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Schiffels J, Selmer T. A flexible toolbox to study protein-assisted metalloenzyme assembly in vitro. Biotechnol Bioeng 2015; 112:2360-72. [PMID: 25994231 DOI: 10.1002/bit.25658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/11/2015] [Indexed: 11/06/2022]
Abstract
A number of metalloenzymes harbor unique cofactors, which are incorporated into the apo-enzymes via protein-assisted maturation. In the case of [NiFe]-hydrogenases, minimally seven maturation factors (HypABCDEF and a specific endopeptidase) are involved, making these enzymes an excellent example for studying metallocenter assembly in general. Here, we describe an innovative toolbox to study maturation involving multiple putative gene products. The two core elements of the system are a modular, combinatorial cloning system and a cell-free maturation system, which is based on recombinant Escherichia coli extracts and/or purified maturases. Taking maturation of the soluble, oxygen-tolerant [NiFe]-hydrogenase (SH) from Cupriavidus necator as an example, the capacities of the toolbox are illustrated. In total 18 genes from C. necator were analyzed, including four SH-structural genes, the SH-dedicated hyp-genes and a second set of hyp-genes putatively involved in maturation of the Actinobacterium-like hydrogenase (AH). The two hyp-sets were either expressed in their entirety from single vectors or split into functional modules, which enabled flexible approaches to investigate limitations, specificities and the capabilities of individual constituents to functionally substitute each other. Affinity-tagged Hyp-Proteins were used in pull-down experiments to demonstrate direct interactions between dedicated or non-related constituents. The dedicated Hyp-set from C. necator exhibited the highest maturation efficiency in vitro. Constituents of non-related maturation machineries were found to interact with and to accomplish partial activation of SH. In contrast to homologues of the Hyp-family, omission of the SH-specific endopeptidase HoxW completely abolished in vitro maturation. We detected stoichiometric imbalances inside the recombinant production system, which point to limitations by the cyanylation complex HypEF and the premature subunit HoxH. Purification of HoxW revealed strong indications for the presence of a putative [4Fe-4S]-cluster, which is unique among this class of maturases. Results are discussed in the context of [NiFe]-hydrogenase maturation, and in light of the capacity of the novel toolbox.
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Affiliation(s)
- Johannes Schiffels
- From the Aachen University of Applied Sciences, Campus Juelich, Department of Chemistry and Biotechnology, Heinrich-Mussmann-Str. 1, D-52428 Juelich, Germany
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15
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Gayomba SR, Zhai Z, Jung HI, Vatamaniuk OK. Local and systemic signaling of iron status and its interactions with homeostasis of other essential elements. FRONTIERS IN PLANT SCIENCE 2015; 6:716. [PMID: 26442030 PMCID: PMC4568396 DOI: 10.3389/fpls.2015.00716] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/27/2015] [Indexed: 05/03/2023]
Abstract
Iron (Fe) is essential for plant growth and development. However, alkaline soils, which occupy approximately 30% of the world's arable lands, are considered Fe-limiting for plant growth because insoluble Fe (III) chelates prevail under these conditions. In contrast, high bioavailability of Fe in acidic soils can be toxic to plants due to the ability of Fe ions to promote oxidative stress. Therefore, plants have evolved sophisticated mechanisms to sense and respond to the fluctuation of Fe availability in the immediate environment and to the needs of developing shoot tissues to preclude deficiency while avoiding toxicity. In this review, we focus on recent advances in our understanding of local and systemic signaling of Fe status with emphasis on the contribution of Fe, its interaction with other metals and metal ligands in triggering molecular responses that regulate Fe uptake and partitioning in the plant body.
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Affiliation(s)
| | | | | | - Olena K. Vatamaniuk
- *Correspondence: Olena K. Vatamaniuk, Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, 360 Tower Road, 608 Bradfield Hall, Ithaca, NY 14853, USA,
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16
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Geethalakshmi KR, Yang X, Sun Q, Ng TY, Wang D. The nature of interfacial binding of imidazole and carbene ligands with M20 nanoclusters (M = Au, Ag and Cu) – a theoretical study. RSC Adv 2015. [DOI: 10.1039/c5ra14578c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To inspire more exciting developments in the design and advances of self-assembled monolayers (SAMs), the fundamental understanding of the nature of interaction between metal nanoparticles and certain functional groups is very crucial.
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Affiliation(s)
- K. R. Geethalakshmi
- Centro de Física de Materiales (CSIC-UPV/EHU) and Donostia International Physics Center (DIPC)
- P. Manuel de Lardizabal 5
- 20018 Donostia
- Spain
- School of Mechanical and Aerospace Engineering
| | - Xia Yang
- Institute of High Energy Physics
- Chinese Academy of Science
- Beijing
- China
| | - Qiao Sun
- Institute of Quantitative Biology and Medicine
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- School of Radiation Medicine and Protection
- Medical College of Soochow University
- Soochow University
| | - T. Y. Ng
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University Singapore
- Singapore-639798
| | - D. Wang
- Institute of High Energy Physics
- Chinese Academy of Science
- Beijing
- China
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17
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Xia W, Li H, Sun H. Functional disruption of HypB, a GTPase of Helicobacter pylori, by bismuth. Chem Commun (Camb) 2014; 50:1611-4. [PMID: 24389922 DOI: 10.1039/c3cc47644h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bismuth (Bi(3+)) binds equal molar amounts of HypB from Helicobacter pylori at the conserved metal site with a dissociation constant of 0.94 (±0.25) × 10(-17) μM, and concomitantly induces the protein dimerization similarly to Ni(2+). Excess Bi(3+) causes HypB further oligomerization, leading to HypB GTPase dysfunction. The results extend our understanding on the inhibitory mechanism of bismuth drugs against the pathogen.
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Affiliation(s)
- Wei Xia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China.
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18
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Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
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19
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Cheng T, Li H, Yang X, Xia W, Sun H. Interaction of SlyD with HypB of Helicobacter pylori facilitates nickel trafficking. Metallomics 2014; 5:804-7. [PMID: 23708681 DOI: 10.1039/c3mt00014a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SlyD from Helicobacter pylori interacts with the [NiFe] hydrogenase accessory protein HypB through its IF domain. HpSlyD delivers Ni(2+) to HpHypB, leading to the enhancement of GTPase activity of HpHypB and implying the facilitation of Ni(2+) delivery from HpHypB to [NiFe] hydrogenase.
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Affiliation(s)
- Tianfan Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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20
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Ge RG, Wang DX, Hao MC, Sun XS. Nickel trafficking system responsible for urease maturation in Helicobacter pylori. World J Gastroenterol 2013; 19:8211-8218. [PMID: 24363511 PMCID: PMC3857443 DOI: 10.3748/wjg.v19.i45.8211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/17/2013] [Accepted: 11/03/2013] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a common human pathogen responsible for various gastric diseases. This bacterium relies on the production of urease and hydrogenase to inhabit the acidic environment of the stomach. Nickel is an essential cofactor for urease and hydrogenase. H. pylori has to uptake sufficient nickel ions for the maturation of urease, and on the other way, to prevent the toxic effects of excessive nickel ions. Therefore, H. pylori has to strike a delicate balance between the import of nickel ions, its efficient intracellular storage, and delivery to nickel-dependent metalloenzymes when required. The assembly and maturation of the urease enzyme is a complex and timely ordered process, requiring various regulatory, uptake, chaperone and accessory proteins. In this review, we focus on several nickel trafficking proteins involved in urease maturation: NikR, NixA, HypAB, UreEFGH, HspA, Hpn and Hpnl. The work will deepen our understanding of how this pathogenic bacterium adapts to severe habitant environments in the host.
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21
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Douglas CD, Ngu TT, Kaluarachchi H, Zamble DB. Metal transfer within the Escherichia coli HypB-HypA complex of hydrogenase accessory proteins. Biochemistry 2013; 52:6030-9. [PMID: 23899293 DOI: 10.1021/bi400812r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The maturation of [NiFe]-hydrogenase in Escherichia coli is a complex process involving many steps and multiple accessory proteins. The two accessory proteins HypA and HypB interact with each other and are thought to cooperate to insert nickel into the active site of the hydrogenase-3 precursor protein. Both of these accessory proteins bind metal individually, but little is known about the metal-binding activities of the proteins once they assemble together into a functional complex. In this study, we investigate how complex formation modulates metal binding to the E. coli proteins HypA and HypB. This work lead to a re-evaluation of the HypA nickel affinity, revealing a KD on the order of 10(-8) M. HypA can efficiently remove nickel, but not zinc, from the metal-binding site in the GTPase domain of HypB, a process that is less efficient when complex formation between HypA and HypB is disrupted. Furthermore, nickel release from HypB to HypA is specifically accelerated when HypB is loaded with GDP, but not GTP. These results are consistent with the HypA-HypB complex serving as a transfer step in the relay of nickel from membrane transporter to its final destination in the hydrogenase active site and suggest that this complex contributes to the metal fidelity of this pathway.
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Affiliation(s)
- Colin D Douglas
- Department of Chemistry, University of Toronto , 80 St. George St., Toronto, Ontario M5S 3H6, Canada
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22
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Ugarte M, Grime GW, Lord G, Geraki K, Collingwood JF, Finnegan ME, Farnfield H, Merchant M, Bailey MJ, Ward NI, Foster PJ, Bishop PN, Osborne NN. Concentration of various trace elements in the rat retina and their distribution in different structures. Metallomics 2013; 4:1245-54. [PMID: 23093062 DOI: 10.1039/c2mt20157g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inductively coupled plasma mass spectrometry (ICP-MS) was used to quantify the total amount of trace elements in retina from adult male Sprague-Dawley rats (n = 6). Concentration of trace elements within individual retinal areas in frozen sections of the fellow eye was established with the use of two methodologies: (1) particle-induced X-ray emission (PIXE) in combination with 3D depth profiling with Rutherford backscattering spectrometry (RBS) and (2) synchrotron X-ray fluorescence (SXRF) microscopy. The most abundant metal in the retina was zinc, followed by iron and copper. Nickel, manganese, chromium, cobalt, selenium and cadmium were present in very small amounts. The PIXE and SXRF analysis yielded a non-homogenous pattern distribution of metals in the retina. Relatively high levels of zinc were found in the inner part of the photoreceptor inner segments (RIS)/outer limiting membrane (OLM), inner nuclear layer and plexiform layers. Iron was found to accumulate in the retinal pigment epithelium/choroid layer and RIS/OLM. Copper in turn, was localised primarily in the RIS/OLM and plexiform layers. The trace elements iron, copper, and zinc exist in different amounts and locations in the rat retina.
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Affiliation(s)
- Marta Ugarte
- Centre for Advanced Discovery and Experimental Therapeutics, Institute of Human Development, University of Manchester and Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PT, UK.
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23
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Cui W, Yang X, Fang Y, Zhou S, Liu S, Du G, Du K, Chen J, Tao G, Zhou Z. Discovery of two transglutaminases derived from same zymogen for the Streptomyces hygroscopicus and analysis of their formation processes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:1711-1717. [PMID: 23355183 DOI: 10.1002/jsfa.5956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/13/2012] [Accepted: 10/19/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Transglutaminase (TGase) is secreted as a zymogen (Pro-TGase) and is then processed by removal of its N-terminal region through exogenous proteolytic activity. In this study it was discovered that the Pro-TGase from Streptomyces hygroscopicus was also activated by its TGase (processed through exogenous proteolytic activity), resulting in a different active form. RESULTS The two TGases exhibited different ionic strengths, hydrophobicities, Km values and stabilities. Circular dichroism spectral analysis showed that the two enzymes had non-identical secondary structures, while liquid chromatography/mass spectrometry (LC-MS) analysis indicated that they differed in molecular mass by 111 Da. The formation of the TGase activated from Pro-TGase by TGase was delayed compared with that of TGase processed through exogenous proteolytic activity. Furthermore, it was found that the TGase activated from Pro-TGase by TGase did not activate Pro-TGase. CONCLUSION Two TGases derived from the same zymogen from S. hygroscopicus were discovered. These two active forms of TGase may be due to different activation processes: one of them is catalysed by its own active TGase, while the other is activated by an exogenous protease.
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Affiliation(s)
- Wenjing Cui
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, China
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24
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25
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Blaby-Haas CE, Flood JA, Crécy-Lagard VD, Zamble DB. YeiR: a metal-binding GTPase from Escherichia coli involved in metal homeostasis. Metallomics 2012; 4:488-97. [PMID: 22511334 DOI: 10.1039/c2mt20012k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A comparative genomic analysis predicted that many members of the under-characterized COG0523 subfamily of putative P-loop GTPases function in metal metabolism. In this work we focused on the uncharacterized Escherichia coli protein YeiR by studying both the physiology of a yeiR mutant and the in vitro biochemical properties of YeiR expressed as a fusion with the maltose-binding protein (YeiR-MBP). Our results demonstrate that deletion of yeiR increases the sensitivity of E. coli to EDTA or cadmium, and this phenotype is linked to zinc depletion. In vitro, the tagged protein binds several Zn(2+) ions with nanomolar affinity and oligomerizes in the presence of metal. The GTPase activity of YeiR is similar to that measured for other members of the group, but GTP hydrolysis is enhanced by Zn(2+) binding. These results support the predicted connection between the COG0523 P-loop GTPases and roles in metal homeostasis.
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Affiliation(s)
- Crysten E Blaby-Haas
- Department of Microbiology & Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611-0700, USA.
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26
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Kaluarachchi H, Altenstein M, Sugumar SR, Balbach J, Zamble DB, Haupt C. Nickel binding and [NiFe]-hydrogenase maturation by the metallochaperone SlyD with a single metal-binding site in Escherichia coli. J Mol Biol 2012; 417:28-35. [PMID: 22310044 DOI: 10.1016/j.jmb.2012.01.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 11/17/2022]
Abstract
SlyD (sensitive to lysis D) is a nickel metallochaperone involved in the maturation of [NiFe]-hydrogenases in Escherichia coli (E. coli) and specifically contributes to the nickel delivery step during enzyme biosynthesis. This protein contains a C-terminal metal-binding domain that is rich in potential metal-binding residues that enable SlyD to bind multiple nickel ions with high affinity. The SlyD homolog from Thermus thermophilus does not contain the extended cysteine- and histidine-rich C-terminal tail of the E. coli protein, yet it binds a single Ni(II) ion tightly. To investigate whether a single metal-binding motif can functionally replace the full-length domain, we generated a truncation of E. coli SlyD, SlyD155. Ni(II) binding to SlyD155 was investigated by using isothermal titration calorimetry, NMR and electrospray ionization mass spectrometry measurements. This in vitro characterization revealed that SlyD155 contains a single metal-binding motif with high affinity for nickel. Structural characterization by X-ray absorption spectroscopy and NMR indicated that nickel was coordinated in an octahedral geometry with at least two histidines as ligands. Heterodimerization between SlyD and another hydrogenase accessory protein, HypB, is essential for optimal hydrogenase maturation and was confirmed for SlyD155 via cross-linking experiments and NMR titrations, as were conserved chaperone and peptidyl-prolyl isomerase activities. Although these properties of SlyD are preserved in the truncated version, it does not modulate nickel binding to HypB in vitro or contribute to the maturation of [NiFe]-hydrogenases in vivo, unlike the full-length protein. This study highlights the importance of the unusual metal-binding domain of E. coli SlyD in hydrogenase biogenesis.
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Affiliation(s)
- Harini Kaluarachchi
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, ON, Canada M5S 3H6
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27
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Fukuzumi S, Ohkubo K, Morimoto Y. Mechanisms of metal ion-coupled electron transfer. Phys Chem Chem Phys 2012; 14:8472-84. [DOI: 10.1039/c2cp40459a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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28
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Douglas CD, Dias AV, Zamble DB. The metal selectivity of a short peptide maquette imitating the high-affinity metal-binding site of E. coli HypB. Dalton Trans 2012; 41:7876-8. [DOI: 10.1039/c2dt30132f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Witkowska D, Rowinska-Zyrek M, Valensin G, Kozlowski H. Specific poly-histidyl and poly-cysteil protein sites involved in Ni2+ homeostasis in Helicobacter pylori. Impact of Bi3+ ions on Ni2+ binding to proteins. Structural and thermodynamic aspects. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.06.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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30
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Abstract
Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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31
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Chan Chung KC, Zamble DB. Protein interactions and localization of the Escherichia coli accessory protein HypA during nickel insertion to [NiFe] hydrogenase. J Biol Chem 2011; 286:43081-90. [PMID: 22016389 DOI: 10.1074/jbc.m111.290726] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nickel delivery during maturation of Escherichia coli [NiFe] hydrogenase 3 includes the accessory proteins HypA, HypB, and SlyD. Although the isolated proteins have been characterized, little is known about how they interact with each other and the hydrogenase 3 large subunit, HycE. In this study the complexes of HypA and HycE were investigated after modification with the Strep-tag II. Multiprotein complexes containing HypA, HypB, SlyD, and HycE were observed, consistent with the assembly of a single nickel insertion cluster. An interaction between HypA and HycE did not require the other nickel insertion proteins, but HypB was not found with the large subunit in the absence of HypA. The HypA-HycE complex was not detected in the absence of the HypC or HypD proteins, involved in the preceding iron insertion step, and this interaction is enhanced by nickel brought into the cell by the NikABCDE membrane transporter. Furthermore, without the hydrogenase 1, 2, and 3 large subunits, complexes between HypA, HypB, and SlyD were observed. These results support the hypothesis that HypA acts as a scaffold for assembly of the nickel insertion proteins with the hydrogenase precursor protein after delivery of the iron center. At different stages of the hydrogenase maturation process, HypA was observed at or near the cell membrane by using fluorescence confocal microscopy, as was HycE, suggesting membrane localization of the nickel insertion event.
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Affiliation(s)
- Kim C Chan Chung
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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32
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Denger K, Lehmann S, Cook AM. Molecular genetics and biochemistry of N-acetyltaurine degradation by Cupriavidus necator H16. MICROBIOLOGY-SGM 2011; 157:2983-2991. [PMID: 21757489 DOI: 10.1099/mic.0.048462-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cupriavidus necator H16 (DSM 428), whose genome has been sequenced, was found to degrade N-acetyltaurine as a sole source of carbon and energy for growth. Utilization of the compound was quantitative. The degradative pathway involved an inducible N-acetyltaurine amidohydrolase (NaaS), which catalysed the cleavage of N-acetyltaurine to acetate and taurine. The degradation of the latter compound is via an inducible, degradative pathway that involves taurine dehydrogenase [EC 1.4.2.-], sulfoacetaldehyde acetyltransferase [EC 2.3.3.15], phosphotransacetylase [EC 2.4.1.8], a sulfite exporter [TC 9.A.29.2.1] and sulfite dehydrogenase [EC 1.8.2.1]. Induction of the expression of representative gene products, encoded by at least four gene clusters, was confirmed biochemically. The acetate released by NaaS was activated to acetyl-CoA by an inducible acetate-CoA ligase [EC 6.2.1.1]. NaaS was purified to homogeneity; it had a K(m) value of 9.4 mM for N-acetyltaurine, and it contained tightly bound Zn and Fe atoms. The denatured enzyme has a molecular mass of about 61 kDa (determined by SDS-PAGE) and the native enzyme was apparently monomeric. Peptide-mass fingerprinting identified the locus tag as H16_B0868 in a five-gene cluster, naaROPST (H16_B0865-H16_B0869). The cluster presumably encodes a LysR-type transcriptional regulator (NaaR), a membrane protein (NaaO), a solute : sodium symporter-family permease [TC 2.A.21] (NaaP), the metal-dependent amidohydrolase (NaaS) and a putative metallochaperone (COG0523) (NaaT). Reverse-transcription PCR indicated that naaOPST were inducibly transcribed.
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Affiliation(s)
- Karin Denger
- Department of Biology, The University, D-78457 Konstanz, Germany
| | - Sabine Lehmann
- Department of Biology, The University, D-78457 Konstanz, Germany
| | - Alasdair M Cook
- Department of Biology, The University, D-78457 Konstanz, Germany
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33
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Relationship between the GTPase, metal-binding, and dimerization activities of E. coli HypB. J Biol Inorg Chem 2011; 16:857-68. [PMID: 21544686 DOI: 10.1007/s00775-011-0782-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
Abstract
Biosynthesis of the metallocenter in the active site of the [NiFe] hydrogenase enzyme requires the accessory protein HypB, which is a metal-binding GTPase. In this study, the interplay between the individual activities of Escherichia coli HypB was examined. The full-length protein undergoes nucleotide-responsive dimerization that is disrupted upon mutation of L242 and L246 to alanine. This mutant HypB is monomeric under all of the conditions investigated but the inability of L242A/L246A HypB to dimerize does not abolish its GTPase activity and the monomeric protein has metal-binding behavior similar to that of wild-type HypB. Furthermore, expression of L242A/L246A HypB in vivo results in hydrogenase activity that is approximately half of the activity produced by the wild-type control, suggesting that dimerization of HypB does not have a critical role in the hydrogenase maturation pathway. In contrast, the GTPase activity of HypB is modulated by metal loading of the protein. These results provide insight into the role of HypB in hydrogenase biosynthesis.
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34
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Bleackley MR, Young BP, Loewen CJR, MacGillivray RTA. High density array screening to identify the genetic requirements for transition metal tolerance in Saccharomyces cerevisiae. Metallomics 2011; 3:195-205. [PMID: 21212869 DOI: 10.1039/c0mt00035c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biological systems have developed with a strong dependence on transition metals for accomplishing a number of biochemical reactions. Iron, copper, manganese and zinc are essential for virtually all forms of life with their unique chemistries contributing to a variety of physiological processes including oxygen transport, generation of cellular energy and protein structure and function. Properties of these metals (and to a lesser extent nickel and cobalt) that make them so essential to life also make them extremely cytotoxic in many cases through the formation of damaging oxygen radicals via Fenton chemistry. While life has evolved to exploit the chemistries of transition metals to drive physiological reactions, systems have concomitantly evolved to protect against the damaging effects of these same metals. Saccharomyces cerevisiae is a valuable tool for studying metal homeostasis with many of the genes identified thus far having homologs in higher eukaryotes including humans. Using high density arrays, we have screened a haploid S. cerevisiae deletion set containing 4786 non-essential gene deletions for strains sensitive to each of Fe, Cu, Mn, Ni, Zn and Co and then integrated the six screens using cluster analysis to identify pathways that are unique to individual metals and others with function shared between metals. Genes with no previous implication in metal homeostasis were found to contribute to sensitivity to each metal. Significant overlap was observed between the strains that were sensitive to Mn, Ni, Zn and Co with many of these strains lacking genes for the high affinity Fe transport pathway and genes involved in vacuolar transport and acidification. The results from six genome-wide metal tolerance screens show that there is some commonality between the cellular defenses against the toxicity of Mn, Ni, Zn and Co with Fe and Cu requiring different systems. Additionally, potential new factors been identified that function in tolerance to each of the six metals.
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Affiliation(s)
- Mark R Bleackley
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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35
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Izzo V, Leo G, Scognamiglio R, Troncone L, Birolo L, Di Donato A. PHK from phenol hydroxylase of Pseudomonas sp. OX1. Insight into the role of an accessory protein in bacterial multicomponent monooxygenases. Arch Biochem Biophys 2011; 505:48-59. [DOI: 10.1016/j.abb.2010.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/06/2010] [Accepted: 09/25/2010] [Indexed: 11/30/2022]
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36
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Hunter GA, Ferreira GC. Identification and characterization of an inhibitory metal ion-binding site in ferrochelatase. J Biol Chem 2010; 285:41836-42. [PMID: 20966079 DOI: 10.1074/jbc.m110.174243] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX to form heme. The severe metal ion substrate inhibition observed during in vitro studies of the purified enzyme is almost completely eliminated by mutation of an active site histidine residue (His-287, murine ferrochelatase numbering) to leucine and reduced over 2 orders of magnitude by mutation of a nearby conserved phenylalanine residue (Phe-283) to leucine. Elimination of substrate inhibition had no effect on the apparent V(max) for Ni(2+), but the apparent K(m) was increased 100-fold, indicating that the integrity of the inhibitory binding site is important for the enzyme to turn over substrates rapidly at low micromolar metal ion concentrations. The inhibitory site was observed to have a pK(a) value of 8.0, and this value was reduced to 7.5 by the F283L mutation and to 7.4 in a naturally occurring positional variant observed in most bacterial ferrochelatases, murine ferrochelatase H287C. A H287N variant was also found to be substrate-inhibited, but unlike the H287C variant, pH dependence of substrate inhibition was largely eliminated. The data indicate that the inhibitory metal ion-binding site is composed of multiple residues but primarily defined by His-287 and Phe-283 and is crucial for optimal activity at low metal ion concentrations. It is proposed that this binding site may be important for ferrous iron acquisition and desolvation in vivo.
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Affiliation(s)
- Gregory A Hunter
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612, USA.
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37
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Zhou Z, Hashimoto Y, Cui T, Washizawa Y, Mino H, Kobayashi M. Unique Biogenesis of High-Molecular Mass Multimeric Metalloenzyme Nitrile Hydratase: Intermediates and a Proposed Mechanism for Self-Subunit Swapping Maturation. Biochemistry 2010; 49:9638-48. [DOI: 10.1021/bi100651v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhemin Zhou
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tianwei Cui
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yumi Washizawa
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroyuki Mino
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Watt RK, Hilton RJ, Graff DM. Oxido-reduction is not the only mechanism allowing ions to traverse the ferritin protein shell. Biochim Biophys Acta Gen Subj 2010; 1800:745-59. [DOI: 10.1016/j.bbagen.2010.03.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Revised: 02/20/2010] [Accepted: 03/01/2010] [Indexed: 01/19/2023]
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39
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Jeoung JH, Giese T, Grünwald M, Dobbek H. Crystal structure of the ATP-dependent maturation factor of Ni,Fe-containing carbon monoxide dehydrogenases. J Mol Biol 2010; 396:1165-79. [PMID: 20064527 DOI: 10.1016/j.jmb.2009.12.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/17/2009] [Accepted: 12/26/2009] [Indexed: 11/26/2022]
Abstract
CooC proteins are ATPases involved in the incorporation of nickel into the complex active site ([Ni-4Fe-4S]) cluster of Ni,Fe-dependent carbon monoxide dehydrogenases. The genome of the carboxydotrophic bacterium Carboxydothermus hydrogenoformans encodes five carbon monoxide dehydrogenases and three CooC-type proteins, of which CooC1 was shown to be a nickel-binding ATPase. We determined the crystal structure of CooC1 in four different states: empty, ADP-bound, Zn(2+)/ADP-bound, and Zn(2+)-bound. The structure of CooC1 consists of two spatially separated functional modules: an ATPase module containing the deviant Walker A motif and a metal-binding module that confers the specific function of CooC1. The ATPase module is homologous to other members of the MinD family and, in analogy to the dimeric structure of ATP-bound Soj, is likely responsible for the ATP-dependent dimerization of CooC1. Its core topology classifies CooC1 as a member of the MinD family of SIMIBI (signal recognition particle, MinD and BioD)-class NTPases. The crystal structure of Zn(2+)-bound CooC1 reveals a conserved C-X-C motif as the metal-binding site responsible for metal-induced dimerization. The competitive binding of Ni(2+) and Zn(2+) to CooC1 in solution confirms that the conserved C-X-C motif is also responsible for the interaction with Ni(2+). A comparison of the different CooC1 structures determined suggests a mutual dependence of metal-binding site and nucleotide-binding site.
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Affiliation(s)
- Jae-Hun Jeoung
- AG Bioanorganische Chemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Affiliation(s)
- Wolfgang Maret
- Department of Preventive Medicine & Community Health, The University of Texas Medical Branch, Galveston, Texas 77555-1109, USA.
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Jeoung JH, Giese T, Grünwald M, Dobbek H. CooC1 from Carboxydothermus hydrogenoformans is a nickel-binding ATPase. Biochemistry 2009; 48:11505-13. [PMID: 19883128 DOI: 10.1021/bi901443z] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The maturation of nickel-dependent enzymes requires the participation of several accessory proteins. Typically the hydrolysis of nucleotides is necessary for the final metal transfer steps. The ATPase CooC has been implicated in the insertion of nickel into the Ni,Fe cluster (C cluster) of the carbon monoxide dehydrogenase from Rhodospirillum rubrum. Analysis of the amino acid sequence of CooC suggests the presence of motifs typical for the MinD family of SIMIBI class NTPases, which contain a deviant Walker A motif. The genome of the carboxidotrophic hydrogenogenic bacterium Carboxydothermus hydrogenoformans contains three open reading frames with distinct sequence homology to CooC from R. rubrum. We overproduced, isolated, and studied CooC1 from C. hydrogenoformans. As-isolated CooC1 is monomeric in the absence of ligands but dimerizes in the presence of either nickel, ADP, or ATP. CooC1 shows ATPase activity, and the ADP- and ATP-bound dimeric states are distinguished by their stability. The K8A mutant of CooC1, in which alanine replaces the signature lysine typical for the deviant Walker A motif in the MinD family, is incapable of both ATP hydrolysis and ATP-dependent dimerization. This corroborates that CooC1 is indeed a member of the MinD family and suggests an analogous dynamic equilibrium between monomeric and dimeric states. CooC proteins are involved in the insertion of nickel into carbon monoxide dehydrogenases, and we found that one CooC1 dimer binds one Ni(II) ion with nanomolar affinity. Ni-induced dimerization and the Ni(II)-CooC1 stoichiometry suggest that the Ni-binding site of CooC1 occurs in the dimer interface.
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Affiliation(s)
- Jae-Hun Jeoung
- Bioinorganic Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
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Kaluarachchi H, Sutherland DEK, Young A, Pickering IJ, Stillman MJ, Zamble DB. The Ni(II)-Binding Properties of the Metallochaperone SlyD. J Am Chem Soc 2009; 131:18489-500. [DOI: 10.1021/ja9081765] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harini Kaluarachchi
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Duncan E. K. Sutherland
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Alex Young
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Ingrid J. Pickering
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Martin J. Stillman
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6, Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7, and Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
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Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crécy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 2009; 10:470. [PMID: 19822009 PMCID: PMC2770081 DOI: 10.1186/1471-2164-10-470] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/12/2009] [Indexed: 11/11/2022] Open
Abstract
Background COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. Results Based on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Conclusion This work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s) might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression of COG0523 and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.
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Affiliation(s)
- Crysten E Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
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Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol 2009; 394:448-59. [PMID: 19769985 DOI: 10.1016/j.jmb.2009.09.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/27/2009] [Accepted: 09/14/2009] [Indexed: 11/23/2022]
Abstract
HypA is one of the auxiliary proteins involved in the maturation of [NiFe] hydrogenases. By an unknown mechanism, HypA functions as a metallochaperone in the insertion of the Ni atom into hydrogenases. We have determined the crystal structures of HypA from Thermococcus kodakaraensis KOD1 in both monomeric and dimeric states. The structure of the HypA monomer consists of Ni- and Zn-binding domains. The relative arrangement of the two metal-binding domains has been shown to be associated with local conformations of the conserved Ni-binding motif, suggesting a communication between the Ni- and Zn-binding sites. The HypA dimer has been shown to be stabilized by unexpected domain swapping through archaea-specific linker helices. In addition, the hexameric structure of HypA is formed in the crystal packing. Several hydrogen bonds and hydrophobic interactions stabilize the hexamer interface. These findings suggest the functional diversity of HypA proteins.
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Nadler A, Hain C, Diederichsen U. Histidine Analog Amino Acids Providing Metal-Binding Sites Derived from Bioinorganic Model Systems. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900472] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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Whittaker JW. Metal uptake by manganese superoxide dismutase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:298-307. [PMID: 19699328 DOI: 10.1016/j.bbapap.2009.08.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/09/2009] [Accepted: 08/12/2009] [Indexed: 12/15/2022]
Abstract
Manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. Many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. In contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the protein and one that is absolutely required for its biological function. Recent work is beginning to provide insight into the mechanisms of metal delivery to manganese superoxide dismutase in vivo and in vitro.
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Affiliation(s)
- James W Whittaker
- Department of Science and Engineering, School of Medicine, Oregon Health and Science University, Beaverton, OR 97006-8921, USA.
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Zhou Z, Hashimoto Y, Kobayashi M. Self-subunit swapping chaperone needed for the maturation of multimeric metalloenzyme nitrile hydratase by a subunit exchange mechanism also carries out the oxidation of the metal ligand cysteine residues and insertion of cobalt. J Biol Chem 2009; 284:14930-8. [PMID: 19346246 DOI: 10.1074/jbc.m808464200] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The incorporation of cobalt into low molecular mass nitrile hydratase (L-NHase) of Rhodococcus rhodochrous J1 has been found to depend on the alpha-subunit exchange between cobalt-free L-NHase (apo-L-NHase lacking oxidized cysteine residues) and its cobalt-containing mediator (holo-NhlAE containing Cys-SO(2)(-) and Cys-SO(-) metal ligands), this novel mode of post-translational maturation having been named self-subunit swapping, and NhlE having been recognized as a self-subunit swapping chaperone (Zhou, Z., Hashimoto, Y., Shiraki, K., and Kobayashi, M. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 14849-14854). We discovered here that cobalt was inserted into both the cobalt-free NhlAE (apo-NhlAE) and the cobalt-free alpha-subunit (apo-alpha-subunit) in an NhlE-dependent manner in the presence of cobalt and dithiothreitol in vitro. Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy analysis revealed that the non-oxidized cysteine residues in apo-NhlAE were post-translationally oxidized after cobalt insertion. These findings suggested that NhlE has two activities, i.e. cobalt insertion and cysteine oxidation. NhlE not only functions as a self-subunit swapping chaperone but also a metallochaperone that includes a redox function. Cobalt insertion and cysteine oxidation occurred under both aerobic and anaerobic conditions when Co(3+) was used as a cobalt donor, suggesting that the oxygen atoms in the oxidized cysteines were derived from water molecules but not from dissolved oxygen. Additionally, we isolated apo-NhlAE after the self-subunit swapping event and found that it was recycled for cobalt transfer into L-NHase.
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Affiliation(s)
- Zhemin Zhou
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Groysman S, Holm RH. Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites. Biochemistry 2009; 48:2310-20. [PMID: 19206188 PMCID: PMC2765533 DOI: 10.1021/bi900044e] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few have even been closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases.
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Affiliation(s)
- Stanislav Groysman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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