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Miller C, Huntoon D, Kaley N, Ogutu I, Fiedler AT, Bennett B, Liu D, Holz R. Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases. J Inorg Biochem 2024; 256:112565. [PMID: 38677005 DOI: 10.1016/j.jinorgbio.2024.112565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Two conserved second-sphere βArg (R) residues in nitrile hydratases (NHase), that form hydrogen bonds with the catalytically essential sulfenic and sulfinic acid ligands, were mutated to Lys and Ala residues in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). Only five of the eight mutants (PtNHase βR52A, βR52K, βR157A, βR157K and ReNHase βR61A) were successfully expressed and purified. Apart from the PtNHase βR52A mutant that exhibited no detectable activity, the kcat values obtained for the PtNHase and ReNHase βR mutant enzymes were between 1.8 and 12.4 s-1 amounting to <1% of the kcat values observed for WT enzymes. The metal content of each mutant was also significantly decreased with occupancies ranging from ∼10 to ∼40%. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzyme, suggest a decrease in the Lewis acidity of the active site metal ion. X-ray crystal structures of the four PtNHase βR mutant enzymes confirmed the mutation and the low active site metal content, while also providing insight into the active site hydrogen bonding network. Finally, DFT calculations suggest that the equatorial sulfenic acid ligand, which has been shown to be the catalytic nucleophile, is protonated in the mutant enzyme. Taken together, these data confirm the necessity of the conserved second-sphere βR residues in the proposed subunit swapping process and post-translational modification of the α-subunit in the α activator complex, along with stabilizing the catalytic sulfenic acid in its anionic form.
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Affiliation(s)
- Callie Miller
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Delanie Huntoon
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Irene Ogutu
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, WI 53233, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Richard Holz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
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2
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Kunkle DE, Skaar EP. Moving metals: How microbes deliver metal cofactors to metalloproteins. Mol Microbiol 2023; 120:547-554. [PMID: 37408317 PMCID: PMC10592388 DOI: 10.1111/mmi.15117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
First row d-block metal ions serve as vital cofactors for numerous essential enzymes and are therefore required nutrients for all forms of life. Despite this requirement, excess free transition metals are toxic. Free metal ions participate in the production of noxious reactive oxygen species and mis-metalate metalloproteins, rendering enzymes catalytically inactive. Thus, bacteria require systems to ensure metalloproteins are properly loaded with cognate metal ions to maintain protein function, while avoiding metal-mediated cellular toxicity. In this perspective we summarize the current mechanistic understanding of bacterial metallocenter maturation with specific emphasis on metallochaperones; a group of specialized proteins that both shield metal ions from inadvertent reactions and distribute them to cognate target metalloproteins. We highlight several recent advances in the field that have implicated new classes of proteins in the distribution of metal ions within bacterial proteins, while speculating on the future of the field of bacterial metallobiology.
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Affiliation(s)
- Dillon E. Kunkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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Song X, Lin S, Hu Z, Liu Y, Deng Y, Tang YZ. Possible functions of CobW domain-containing (CBWD) genes in dinoflagellates using Karlodinium veneficum as a representative. HARMFUL ALGAE 2022; 117:102274. [PMID: 35944961 DOI: 10.1016/j.hal.2022.102274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Since > 91% of dinoflagellates are proven auxotrophs of vitamin B12 and the cobalamin synthetase W (CobW) is a key gene involved in vitamin B12 synthesis pathway, a number of CobW domain-containing (CBWD) genes in dinoflagellates (DinoCBWDs) were surprisedly found from our transcriptomic and meta-transcriptomic studies. A total of 88 DinoCBWD genes were identified from the genomes and transcriptomes of four dinoflagellates, with five being cloned for full-lengths and characterized using the cosmopolitan and ecologically-important dinoflagellates Karlodinium veneficum and Scrippsiella trochoidea (synonym of Scrippsiella acuminata). DinoCBWDs were verified being irrelevant to vitamin B12 biosynthesis due to their transcriptions irresponsive to vitamin B12 levels and their phylogenetic positions. A comprehensive phylogenetic analysis demonstrated 75 out of the 88 DinoCBWD genes identified belong to three subfamilies of COG0523 protein family, of which most prokaryotic members are reported to be metallochaperones and the eukaryotic members are ubiquitously found but mostly unknown for their functions. Our results from K. veneficum demonstrated DinoCBWDs are associated with metal homeostasis and other divergent functions, with four KvCBWDs involving in zinc homeostasis and KvCBWD1 likely functioning as Fe-type nitrile hydratase activator. In addition, conserved motif analysis revealed the structural foundation of KvCBWD proteins that are consistent with previously described CBWD proteins with GTPase activity and metal binding. Our results provide a stepping-stone toward better understanding the functions of DinoCBWDs and the COG0523 family.
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Affiliation(s)
- Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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4
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Xia Y, Cheng Z, Hou C, Peplowski L, Zhou Z, Chen X. Discovery of the ATPase Activity of a Cobalt-Type Nitrile Hydratase Activator and Its Promoting Effect on Enzyme Maturation. Biochemistry 2022; 61:2940-2947. [PMID: 35673797 DOI: 10.1021/acs.biochem.2c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An activator protein and a metal ion are two factors known to be indispensable for the maturation of nitrile hydratase (NHase). Here, the third key factor, adenosine triphosphate (ATP), was identified to play an important role in the activation of Co-type NHase. Free phosphate measurements revealed that the Co-type activator protein can hydrolyze ATP/GTP with appreciable performance and that such catalytic performance is related to NHase activity. Computational analysis and site-directed mutagenesis identified several potential hot spot residues involved in the binding of ATP to Co-type activator protein, and an E60A/W61A/D62A/I139A/T141A combinatorial variant reduced the ATPase activity to 18% of its original level. Further NHase activation studies using the combinatorial variant demonstrated that although the ATPase activity of the Co-type activator protein correlated with NHase activity, a low ATP concentration of 0.5 mmol/L was optimal for NHase activation, with higher ATP concentrations potentially inhibiting NHase activity.
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Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chen Hou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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5
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Vaccaro FA, Drennan CL. The role of nucleoside triphosphate hydrolase metallochaperones in making metalloenzymes. Metallomics 2022; 14:6575898. [PMID: 35485745 PMCID: PMC9164220 DOI: 10.1093/mtomcs/mfac030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022]
Abstract
Metalloenzymes catalyze a diverse set of challenging chemical reactions that are essential for life. These metalloenzymes rely on a wide range of metallocofactors, from single metal ions to complicated metallic clusters. Incorporation of metal ions and metallocofactors into apo-proteins often requires the assistance of proteins known as metallochaperones. Nucleoside triphosphate hydrolases (NTPases) are one important class of metallochaperones and are found widely distributed throughout the domains of life. These proteins use the binding and hydrolysis of nucleoside triphosphates, either adenosine triphosphate (ATP) or guanosine triphosphate (GTP), to carry out highly specific and regulated roles in the process of metalloenzyme maturation. Here, we review recent literature on NTPase metallochaperones and describe the current mechanistic proposals and available structural data. By using representative examples from each type of NTPase, we also illustrate the challenges in studying these complicated systems. We highlight open questions in the field and suggest future directions. This minireview is part of a special collection of articles in memory of Professor Deborah Zamble, a leader in the field of nickel biochemistry.
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Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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6
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Edmonds KA, Jordan MR, Giedroc DP. COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man. Metallomics 2021; 13:6327566. [PMID: 34302342 PMCID: PMC8360895 DOI: 10.1093/mtomcs/mfab046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023]
Abstract
Transition metal homeostasis ensures that cells and organisms obtain sufficient metal to meet cellular demand while dispensing with any excess so as to avoid toxicity. In bacteria, zinc restriction induces the expression of one or more Zur (zinc-uptake repressor)-regulated Cluster of Orthologous Groups (COG) COG0523 proteins. COG0523 proteins encompass a poorly understood sub-family of G3E P-loop small GTPases, others of which are known to function as metallochaperones in the maturation of cobalamin (CoII) and NiII cofactor-containing metalloenzymes. Here, we use genomic enzymology tools to functionally analyse over 80 000 sequences that are evolutionarily related to Acinetobacter baumannii ZigA (Zur-inducible GTPase), a COG0523 protein and candidate zinc metallochaperone. These sequences segregate into distinct sequence similarity network (SSN) clusters, exemplified by the ZnII-Zur-regulated and FeIII-nitrile hydratase activator CxCC (C, Cys; X, any amino acid)-containing COG0523 proteins (SSN cluster 1), NiII-UreG (clusters 2, 8), CoII-CobW (cluster 4), and NiII-HypB (cluster 5). A total of five large clusters that comprise ≈ 25% of all sequences, including cluster 3 which harbors the only structurally characterized COG0523 protein, Escherichia coli YjiA, and many uncharacterized eukaryotic COG0523 proteins. We also establish that mycobacterial-specific protein Y (Mpy) recruitment factor (Mrf), which promotes ribosome hibernation in actinomycetes under conditions of ZnII starvation, segregates into a fifth SSN cluster (cluster 17). Mrf is a COG0523 paralog that lacks all GTP-binding determinants as well as the ZnII-coordinating Cys found in CxCC-containing COG0523 proteins. On the basis of this analysis, we discuss new perspectives on the COG0523 proteins as cellular reporters of widespread nutrient stress induced by ZnII limitation.
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Affiliation(s)
- Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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7
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Shen JD, Cai X, Wang M, Liu ZQ, Zheng YG. Proposed mechanism for post-translational self-modification of Co-NHase based on Co 2+ diffusion limitation. Biotechnol J 2021; 16:e2100103. [PMID: 34363653 DOI: 10.1002/biot.202100103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Nitrile hydratase (NHase), was an excellent biocatalyst for the synthesis of amide compounds. NHase was typical heterodimeric metalloprotein, required of the assistance of activator for active expressions. In this work, we found a special Co-NHase HBA from Caldalkalibacillus thermarum, which had the ability of post-translational self-modification and could incorporate Co2+ into the catalytic center in the absence of activator. METHOD AND RESULTS We simulated the movement of Co2+ in silico and established a hypothetical model to predict the Co2+ incorporation efficiency (XCo ) of NHases. According to the simulation results, NHase mutants with different positive charge distribution were constructed. Compared with wild-type, the Co2+ incorporation efficiency of K1 (M10K) was increased by 2.1-fold from 0.36 to 0.76, and the specific activity was increased by 3.2-fold from 136.3 to 432.0 U/mg, while mutant K1H1 (M10K, D11H) and K2H2 (M10K, D11H, E20K, N21H) lost the ability of post-translation self-modification. CONCLUSIONS AND IMPLICATIONS The interactions of positively charged residues near the catalytic center, such as lysine with strong electrostatic repulsive interaction, arginine with weak electrostatic repulsive interaction and histidine with metal affinity, could limit the free diffusion of Co2+ in NHase and affect the efficiency of post-translational self-modification. This work also provided an effective strategy for protein engineering of NHases and other metalloenzymes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ji-Dong Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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8
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Calculating metalation in cells reveals CobW acquires Co II for vitamin B 12 biosynthesis while related proteins prefer Zn II. Nat Commun 2021; 12:1195. [PMID: 33608553 PMCID: PMC7895991 DOI: 10.1038/s41467-021-21479-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/25/2021] [Indexed: 02/01/2023] Open
Abstract
Protein metal-occupancy (metalation) in vivo has been elusive. To address this challenge, the available free energies of metals have recently been determined from the responses of metal sensors. Here, we use these free energy values to develop a metalation-calculator which accounts for inter-metal competition and changing metal-availabilities inside cells. We use the calculator to understand the function and mechanism of GTPase CobW, a predicted CoII-chaperone for vitamin B12. Upon binding nucleotide (GTP) and MgII, CobW assembles a high-affinity site that can obtain CoII or ZnII from the intracellular milieu. In idealised cells with sensors at the mid-points of their responses, competition within the cytosol enables CoII to outcompete ZnII for binding CobW. Thus, CoII is the cognate metal. However, after growth in different [CoII], CoII-occupancy ranges from 10 to 97% which matches CobW-dependent B12 synthesis. The calculator also reveals that related GTPases with comparable ZnII affinities to CobW, preferentially acquire ZnII due to their relatively weaker CoII affinities. The calculator is made available here for use with other proteins.
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9
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Hashimoto Y, Ube Y, Doi S, Kumano T, Kobayashi M. Metal chaperone, NhpC, involved in the metallocenter biosynthesis of nitrile hydratase. J GEN APPL MICROBIOL 2021; 67:24-32. [DOI: 10.2323/jgam.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Yuko Ube
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Shiori Doi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Takuto Kumano
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
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10
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Lankathilaka KPW, Bennett B, Holz RC. The Fe-type nitrile hydratase from Rhodococcus equi TG328-2 forms an alpha-activator protein complex. J Biol Inorg Chem 2020; 25:903-911. [DOI: 10.1007/s00775-020-01806-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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11
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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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12
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Jordan MR, Wang J, Weiss A, Skaar EP, Capdevila DA, Giedroc DP. Mechanistic Insights into the Metal-Dependent Activation of Zn II-Dependent Metallochaperones. Inorg Chem 2019; 58:13661-13672. [PMID: 31247880 DOI: 10.1021/acs.inorgchem.9b01173] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Members of the COG0523 subfamily of candidate GTPase metallochaperones function in bacterial transition-metal homeostasis, but the nature of the cognate metal, mechanism of metal transfer, and identification of target protein(s) for metal delivery remain open questions. Here, we explore the multifunctionality of members of the subfamily linked to delivering ZnII to apoprotein targets under conditions of host-imposed transition-metal depletion. We examine two zinc-uptake repressor (Zur)-regulated COG0523 family members, each from a major human pathogen, Acinetobacter baumannii (AbZigA) and Staphylococcus aureus (SaZigA), in an effort to develop a model for ZnII metallochaperone activity. ZnII chelator competition experiments reveal one high-affinity (KZn1 ≈ 1010-1011 M-1) metal-binding site in each GTPase, while AbZigA and SaZigA are characterized by an additional one and two (lower-affinity) metal-binding sites, respectively. CoII titrations reveal that both metallochaperones have similar electronic absorption characteristics that indicate the presence of two tetrahedral metal coordination sites. High-affinity metal binding at the CXCC motif activates the GTPase activity of both enzymes, with ZnII more effective than CoII. Both GTPases bind the product, GDP, more tightly in the apoprotein than the ZnII-bound state and exhibit what is best described as a "locked" conformation around the GTP substrate. Negative thermodynamic linkage is observed between nucleotide binding and metal binding, leading to a new mechanistic model for COG0523-catalyzed metal delivery.
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Affiliation(s)
| | | | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
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13
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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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14
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Metallochaperones and metalloregulation in bacteria. Essays Biochem 2017; 61:177-200. [PMID: 28487396 DOI: 10.1042/ebc20160076] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Bacterial transition metal homoeostasis or simply 'metallostasis' describes the process by which cells control the intracellular availability of functionally required metal cofactors, from manganese (Mn) to zinc (Zn), avoiding both metal deprivation and toxicity. Metallostasis is an emerging aspect of the vertebrate host-pathogen interface that is defined by a 'tug-of-war' for biologically essential metals and provides the motivation for much recent work in this area. The host employs a number of strategies to starve the microbial pathogen of essential metals, while for others attempts to limit bacterial infections by leveraging highly competitive metals. Bacteria must be capable of adapting to these efforts to remodel the transition metal landscape and employ highly specialized metal sensing transcriptional regulators, termed metalloregulatory proteins,and metallochaperones, that allocate metals to specific destinations, to mediate this adaptive response. In this essay, we discuss recent progress in our understanding of the structural mechanisms and metal specificity of this adaptive response, focusing on energy-requiring metallochaperones that play roles in the metallocofactor active site assembly in metalloenzymes and metallosensors, which govern the systems-level response to metal limitation and intoxication.
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