1
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Chivers PT, Basak P, Maroney MJ. One His, two His…the emerging roles of histidine in cellular nickel trafficking. J Inorg Biochem 2024; 259:112668. [PMID: 39053077 DOI: 10.1016/j.jinorgbio.2024.112668] [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: 04/29/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Biological environments present a complex array of metal-binding ligands. Metal-binding proteins have been the overwhelming focus of study because of their important and well-defined biological roles. Consequently, the presence of functional low molecular weight (LMW) metal-ligand complexes has been overlooked in terms of their roles in metallobiochemistry, particularly within cells. Recent studies in microbial systems have illuminated the different roles of L-histidine in nickel uptake, gene expression, and metalloenzyme maturation. In this focused critical review, these roles are surveyed in the context of the coordination chemistry of Ni(II) ions and the amino acid histidine, and the physico-chemical properties of nickel complexes of histidine. These complexes are fundamentally important to cellular metal homeostasis and further work is needed to fully define their contributions.
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Affiliation(s)
- Peter T Chivers
- Departments of Biosciences and Chemistry, University of Durham, Durham DH1 3LE, UK
| | - Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA 01002, United States of America
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA 01002, United States of America.
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2
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Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH, Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Delivering a toxic metal to the active site of urease. SCIENCE ADVANCES 2023; 9:eadf7790. [PMID: 37083535 PMCID: PMC10121161 DOI: 10.1126/sciadv.adf7790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Urease is a nickel (Ni) enzyme that is essential for the colonization of Helicobacter pylori in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of H. pylori UreFD/urease and Klebsiella pneumoniae UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
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Affiliation(s)
- Yap Shing Nim
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ivan Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Longson Tsz Hin Pang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nicholas Man Hon Yuen
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tin Long Chris Ng
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tung Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yakie Yat Hei Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Susan M. Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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Xiong Z, Zhang N, Xu L, Deng Z, Limwachiranon J, Guo Y, Han Y, Yang W, Scharf DH. Urease of Aspergillus fumigatus Is Required for Survival in Macrophages and Virulence. Microbiol Spectr 2023; 11:e0350822. [PMID: 36916906 PMCID: PMC10100864 DOI: 10.1128/spectrum.03508-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 03/16/2023] Open
Abstract
The number of patients suffering from fungal diseases has constantly increased during the last decade. Among the fungal pathogens, the airborne filamentous fungus Aspergillus fumigatus can cause chronic and fatal invasive mold infections. So far, only three major classes of drugs (polyenes, azoles, and echinocandins) are available for the treatment of life-threatening fungal infections, and all present pharmacological drawbacks (e.g., low solubility or toxicity). Meanwhile, clinical antifungal-resistant isolates are continuously emerging. Therefore, there is a high demand for novel antifungal drugs, preferentially those that act on new targets. We studied urease and the accessory proteins in A. fumigatus to determine their biochemical roles and their influence on virulence. Urease is crucial for the growth on urea as the sole nitrogen source, and the transcript and protein levels are elevated on urea media. The urease deficient mutant displays attenuated virulence, and its spores are more susceptible to macrophage-mediated killing. We demonstrated that this observation is associated with an inability to prevent the acidification of the phagosome. Furthermore, we could show that a nickel-chelator inhibits growth on urea. The nickel chelator is also able to reverse the effects of urease on macrophage killing and phagosome acidification, thereby reducing virulence in systemic and trachea infection models. IMPORTANCE The development of antifungal drugs is an urgent task, but it has proven to be difficult due to many similarities between fungal and animal cells. Here, we characterized the urease system in A. fumigatus, which depends on nickel for activity. Notably, nickel is not a crucial element for humans. Therefore, we went further to explore the role of nickel-dependent urease in host-pathogen interactions. We were able to show that urease is important in preventing the acidification of the phagosome and therefore reduces the killing of conidia by macrophages. Furthermore, the deletion of urease shows reduced virulence in murine infection models. Taken together, we identified urease as an essential virulence factor of A. fumigatus. We were able to show that the application of the nickel-chelator dimethylglyoxime is effective in both in vitro and in vivo infection models. This suggests that nickel chelators or urease inhibitors are potential candidates for the development of novel antifungal drugs.
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Affiliation(s)
- Zhenzhen Xiong
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Nan Zhang
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Liru Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiduo Deng
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jarukitt Limwachiranon
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaojie Guo
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Han
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Yang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daniel H. Scharf
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou, China
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4
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Zambelli B, Basak P, Hu H, Piccioli M, Musiani F, Broll V, Imbert L, Boisbouvier J, Maroney MJ, Ciurli S. The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex. Metallomics 2023; 15:mfad003. [PMID: 36638839 PMCID: PMC10001889 DOI: 10.1093/mtomcs/mfad003] [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: 09/15/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.
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Affiliation(s)
- Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Priyanka Basak
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Heidi Hu
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Mario Piccioli
- Centre for Magnetic Resonance, Department of Chemistry, University of Florence, Florence Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Michael J Maroney
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Centre for Magnetic Resonance, Department of Chemistry, University of Florence, Florence Italy
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5
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Abstract
Hydrogenases and ureases play vital metabolic functions in all three domains of life. However, nickel ions are cytotoxic because they can inactivate enzymes that require less competitive ions (e.g. Mg2+) in the Irving-Williams series to function. Life has evolved elegant mechanisms to solve the problem of delivering the toxic metal to the active site of nickel-containing enzymes inside the cells. Here, we review our current understanding of nickel trafficking along the hydrogenase and urease maturation pathways. Metallochaperones and accessory proteins (SlyD, HypA, HypB, UreD, UreE, UreF, and UreG) form specific protein complexes to allow the transfer of nickel from one protein to another without releasing the toxic metal into the cytoplasm. The role of SlyD is not fully understood, but it can interact with and transfer its nickel to HypB. In the hydrogenase maturation pathway, nickel is transferred from HypB to HypA, which can then deliver its nickel to the hydrogenase large subunit precursor. In Helicobacter pylori, the urease maturation pathway receives its nickel from HypA of the hydrogenase maturation pathway via the formation of a HypA/UreE2 complex. Guanosine triphosphate (GTP) binding promotes the formation of a UreE2G2 complex, where UreG receives a nickel from UreE. In the final step of the urease maturation, nickel/GTP-bound UreG forms an activation complex with UreF, UreD, and apo-urease. Upon GTP hydrolysis, nickel is released from UreG to the urease. Finally, some common themes learned from the hydrogenase-urease maturation pathway are discussed.
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Affiliation(s)
- Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Nickel as a virulence factor in the Class I bacterial carcinogen, Helicobacter pylori. Semin Cancer Biol 2021; 76:143-155. [PMID: 33865991 DOI: 10.1016/j.semcancer.2021.04.009] [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: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 01/16/2023]
Abstract
Helicobacter pylori is a human bacterial pathogen that causes peptic ulcers and has been designated a Class I carcinogen by the International Agency for Research on Cancer (IARC). Its ability to survive in the acid environment of the stomach, to colonize the stomach mucosa, and to cause cancer, are linked to two enzymes that require nickel-urease and hydrogenase. Thus, nickel is an important virulence factor and the proteins involved in nickel trafficking are potential antibiotic targets. This review summarizes the nickel biochemistry of H. pylori with a focus on the roles of nickel in virulence, nickel homeostasis, maturation of urease and hydrogenase, and the unique nickel trafficking that occurs between the hydrogenase maturation pathway and urease nickel incorporation that is mediated by the metallochaperone HypA and its partner, HypB.
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7
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Zhang X, Zhao S, He Y, Zheng N, Yan X, Wang J. Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome. Int J Biol Macromol 2020; 161:1591-1601. [PMID: 32755703 DOI: 10.1016/j.ijbiomac.2020.07.260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 11/17/2022]
Abstract
Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE2-2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors.
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Affiliation(s)
- Xiaoyin Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue He
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianghua Yan
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
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8
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Zambelli B, Mazzei L, Ciurli S. Intrinsic disorder in the nickel-dependent urease network. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:307-330. [DOI: 10.1016/bs.pmbts.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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9
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Anderl A, Kolmar H, Fuchsbauer HL. The metal-binding properties of the long chaplin from Streptomyces mobaraensis: A bioinformatic and biochemical approach. J Inorg Biochem 2019; 202:110878. [PMID: 31698184 DOI: 10.1016/j.jinorgbio.2019.110878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Chaplins are amphiphilic proteins coating the surface of aerial hyphae under formation of amyloid-like rodlet layers in streptomycetes. The long chaplin from Streptomyces mobaraensis, Sm-Chp1, harbors extended histidine-rich stretches allowing protein attachment to metal affinity resins. A comprehensive BLASTP search revealed similarity with many putative metal-binding proteins but the deduced sequence motifs were not shared by histidine-rich domains of well-studied proteins. Biochemical analyses showed affinity of Sm-Chp1 for Ni2+, Cu2+ and Zn2+, a binding capacity of 7-8 metal ions, and dissociation constants in a double digit micromolar range. The occurrence of genes for membrane-bound metal transporters and several intra- and extracellular metalloenzymes in the genome of S. mobaraensis suggests that Sm-Chp1 may be a novel type of translocase shifting metals across the rodlet layer from the environment into the cell wall.
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Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany; Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany.
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Abstract
Nickel is essential for the survival of many pathogenic bacteria. E. coli and H. pylori require nickel for [NiFe]-hydrogenases. H. pylori also requires nickel for urease. At high concentrations nickel can be toxic to the cell, therefore, nickel concentrations are tightly regulated. Metalloregulators help to maintain nickel concentration in the cell by regulating the expression of the genes associated with nickel import and export. Nickel import into the cell, delivery of nickel to target proteins, and export of nickel from the cell is a very intricate and well-choreographed process. The delivery of nickel to [NiFe]-hydrogenase and urease is complex and involves several chaperones and accessory proteins. A combination of biochemical, crystallographic, and spectroscopic techniques has been utilized to study the structures of these proteins, as well as protein-protein interactions resulting in an expansion of our knowledge regarding how these proteins sense and bind nickel. In this review, recent advances in the field will be discussed, focusing on the metal site structures of nickel bound to metalloregulators and chaperones.
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11
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Abstract
Maturation of urease involves post-translational insertion of nickel ions to form an active site with a carbamylated lysine ligand and is assisted by urease accessory proteins UreD, UreE, UreF and UreG. Here, we review our current understandings on how these urease accessory proteins facilitate the urease maturation. The urease maturation pathway involves the transfer of Ni2+ from UreE → UreG → UreF/UreD → urease. To avoid the release of the toxic metal to the cytoplasm, Ni2+ is transferred from one urease accessory protein to another through specific protein–protein interactions. One central theme depicts the role of guanosine triphosphate (GTP) binding/hydrolysis in regulating the binding/release of nickel ions and the formation of the protein complexes. The urease and [NiFe]-hydrogenase maturation pathways cross-talk with each other as UreE receives Ni2+ from hydrogenase maturation factor HypA. Finally, the druggability of the urease maturation pathway is reviewed.
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12
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Huang HT, Maroney MJ. Ni(II) Sensing by RcnR Does Not Require an FrmR-Like Intersubunit Linkage. Inorg Chem 2019; 58:13639-13653. [PMID: 31247878 DOI: 10.1021/acs.inorgchem.9b01096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E. coli RcnR (resistance to cobalt and nickel regulator) is a homotetrameric DNA binding protein that regulates the expression of a Ni(II) and Co(II) exporter (RcnAB) by derepressing expression of rcnA and rcnB in response to binding Co(II) or Ni(II). Prior studies have shown that the cognate metal ions, Ni(II) and Co(II), bind in six-coordinate sites at subunit interfaces and are distinguished from noncognate metals (Cu(I), Cu(II), and Zn(II)) by coordination number and ligand selection. In analogy with FrmR, a formaldehyde-responsive transcriptional regulator in the RcnR/CsoR family, the interfacial site allows the metal ions to "cross-link" the N-terminal domain of one subunit with the invariant Cys35 residue in another, which has been deemed to be key to mediating the allosteric response of the tetrameric protein to metal binding. Through the use of mutagenesis to disconnect one subunit from the metal-mediated cross-link, X-ray absorption spectroscopy (XAS) as a structural probe, LacZ reporter assays, and metal binding studies using isothermal titration calorimetry (ITC), the work presented here shows that neither the interfacial binding site nor the coordination number of Ni(II) is important to the allosteric response to binding of this cognate metal ion. The opposite is found for the other cognate metal ion, Co(II), with respect to the interfacial binding site, suggesting that the molecular mechanisms for transcriptional regulation by the two ions are distinct. The metal binding studies reveal that tight metal binding is maintained in the variant. XAS is further used to demonstrate that His33 is not a ligand for Co(II), Ni(II), or Zn(II) in WT-RcnR. The results are discussed in the context of the overall understanding of the molecular mechanisms of metallosensors.
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13
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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14
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Alfano M, Pérard J, Carpentier P, Basset C, Zambelli B, Timm J, Crouzy S, Ciurli S, Cavazza C. The carbon monoxide dehydrogenase accessory protein CooJ is a histidine-rich multidomain dimer containing an unexpected Ni(II)-binding site. J Biol Chem 2019; 294:7601-7614. [PMID: 30858174 DOI: 10.1074/jbc.ra119.008011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/09/2019] [Indexed: 01/14/2023] Open
Abstract
Activation of nickel enzymes requires specific accessory proteins organized in multiprotein complexes controlling metal transfer to the active site. Histidine-rich clusters are generally present in at least one of the metallochaperones involved in nickel delivery. The maturation of carbon monoxide dehydrogenase in the proteobacterium Rhodospirillum rubrum requires three accessory proteins, CooC, CooT, and CooJ, dedicated to nickel insertion into the active site, a distorted [NiFe3S4] cluster coordinated to an iron site. Previously, CooJ from R. rubrum (RrCooJ) has been described as a nickel chaperone with 16 histidines and 2 cysteines at its C terminus. Here, the X-ray structure of a truncated version of RrCooJ, combined with small-angle X-ray scattering data and a modeling study of the full-length protein, revealed a homodimer comprising a coiled coil with two independent and highly flexible His tails. Using isothermal calorimetry, we characterized several metal-binding sites (four per dimer) involving the His-rich motifs and having similar metal affinity (KD = 1.6 μm). Remarkably, biophysical approaches, site-directed mutagenesis, and X-ray crystallography uncovered an additional nickel-binding site at the dimer interface, which binds Ni(II) with an affinity of 380 nm Although RrCooJ was initially thought to be a unique protein, a proteome database search identified at least 46 bacterial CooJ homologs. These homologs all possess two spatially separated nickel-binding motifs: a variable C-terminal histidine tail and a strictly conserved H(W/F)X 2HX 3H motif, identified in this study, suggesting a dual function for CooJ both as a nickel chaperone and as a nickel storage protein.
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Affiliation(s)
- Marila Alfano
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Julien Pérard
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Philippe Carpentier
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Christian Basset
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Barbara Zambelli
- the Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, I-40127 Bologna, Italy
| | - Jennifer Timm
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Serge Crouzy
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
| | - Stefano Ciurli
- the Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, I-40127 Bologna, Italy
| | - Christine Cavazza
- From the Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France and
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15
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Spronk CAEM, Żerko S, Górka M, Koźmiński W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. J Biol Inorg Chem 2018; 23:1309-1330. [PMID: 30264175 DOI: 10.1007/s00775-018-1616-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/05/2018] [Indexed: 01/03/2023]
Abstract
Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.
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Affiliation(s)
- Chris A E M Spronk
- JSC Spronk, Vilnius, Lithuania.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Mario Piccioli
- Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy
| | - Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Faith C Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ryan C Johnson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Heidi Hu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Michael Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. .,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.
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16
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Chaplin VD, Hangasky JA, Huang HT, Duan R, Maroney MJ, Knapp MJ. Chloride Supports O 2 Activation in the D201G Facial Triad Variant of Factor-Inhibiting Hypoxia Inducible Factor, an α-Ketoglutarate Dependent Oxygenase. Inorg Chem 2018; 57:12588-12595. [PMID: 30252455 DOI: 10.1021/acs.inorgchem.8b01736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
α-Ketoglutarate (αKG) dependent oxygenases comprise a large superfamily of enzymes that activate O2 for varied reactions. While most of these enzymes contain a nonheme Fe bound by a His2(Asp/Glu) facial triad, a small number of αKG-dependent halogenases require only the two His ligands to bind Fe and activate O2. The enzyme "factor inhibiting HIF" (FIH) contains a His2Asp facial triad and selectively hydroxylates polypeptides; however, removal of the Asp ligand in the Asp201→Gly variant leads to a highly active enzyme, seemingly without a complete facial triad. Herein, we report on the formation of an Fe-Cl cofactor structure for the Asp201→Gly FIH variant using X-ray absorption spectroscopy (XAS), which provides insight into the structure of the His2Cl facial triad found in halogenases. The Asp201→Gly variant supports anion dependent peptide hydroxylation, demonstrating the requirement for a complete His2X facial triad to support O2 reactivity. Our results indicated that exogenous ligand binding to form a complete His2X facial triad was essential for O2 activation and provides a structural model for the His2Cl-bound nonheme Fe found in halogenases.
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Affiliation(s)
- Vanessa D Chaplin
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - John A Hangasky
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Hsin-Ting Huang
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Ran Duan
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Maroney
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Knapp
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
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17
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Hu HQ, Huang HT, Maroney MJ. The Helicobacter pylori HypA·UreE 2 Complex Contains a Novel High-Affinity Ni(II)-Binding Site. Biochemistry 2018; 57:2932-2942. [PMID: 29708738 DOI: 10.1021/acs.biochem.8b00127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Helicobacter pylori is a human pathogen that colonizes the stomach, is the major cause of ulcers, and has been associated with stomach cancers. To survive in the acidic environment of the stomach, H. pylori uses urease, a nickel-dependent enzyme, to produce ammonia for maintenance of cellular pH. The bacteria produce apo-urease in large quantities and activate it by incorporating nickel under acid shock conditions. Urease nickel incorporation requires the urease-specific metallochaperone UreE and the (UreFGH)2 maturation complex. In addition, the H. pylori nickel urease maturation pathway recruits accessory proteins from the [NiFe] hydrogenase maturation pathway, namely, HypA and HypB. HypA and UreE dimers (UreE2) are known to form a protein complex, the role of which in urease maturation is largely unknown. Herein, we examine the nickel-binding properties and protein-protein interactions of HypA and UreE2 using isothermal titration calorimetry and fluorometric methods under neutral and acidic pH conditions to gain insight into the roles played by HypA in urease maturation. The results reveal that HypA and UreE2 form a stable complex with micromolar affinity that protects UreE from hydrolytic degradation. The HypA·UreE2 complex contains a unique high-affinity (nanomolar) Ni2+-binding site that is maintained under conditions designed to mimic acid shock (pH 6.3). The data are interpreted in terms of a proposed mechanism wherein HypA and UreE2 act as co-metallochaperones that target the delivery of Ni2+ to apo-urease with high fidelity.
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18
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Serrano-Plana J, Acuña-Parés F, Dantignana V, Oloo WN, Castillo E, Draksharapu A, Whiteoak CJ, Martin-Diaconescu V, Basallote MG, Luis JM, Que L, Costas M, Company A. Acid-Triggered O-O Bond Heterolysis of a Nonheme Fe III (OOH) Species for the Stereospecific Hydroxylation of Strong C-H Bonds. Chemistry 2018; 24:5331-5340. [PMID: 29193378 DOI: 10.1002/chem.201704851] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/11/2022]
Abstract
A novel hydroperoxoiron(III) species [FeIII (OOH)(MeCN)(PyNMe3 )]2+ (3) has been generated by reaction of its ferrous precursor [FeII (CF3 SO3 )2 (PyNMe3 )] (1) with hydrogen peroxide at low temperatures. This species has been characterized by several spectroscopic techniques and cryospray mass spectrometry. Similar to most of the previously described low-spin hydroperoxoiron(III) compounds, 3 behaves as a sluggish oxidant and it is not kinetically competent for breaking weak C-H bonds. However, triflic acid addition to 3 causes its transformation into a much more reactive compound towards organic substrates that is capable of oxidizing unactivated C-H bonds with high stereospecificity. Stopped-flow kinetic analyses and theoretical studies provide a rationale for the observed chemistry, a triflic-acid-assisted heterolytic cleavage of the O-O bond to form a putative strongly oxidizing oxoiron(V) species. This mechanism is reminiscent to that observed in heme systems, where protonation of the hydroperoxo intermediate leads to the formation of the high-valent [(Porph. )FeIV (O)] (Compound I).
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Affiliation(s)
- Joan Serrano-Plana
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Ferran Acuña-Parés
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avinguda Països Catalans 16, 43007, Tarragona, Spain
| | - Valeria Dantignana
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Williamson N Oloo
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Esther Castillo
- Departamento de Ciencia de los Materiales e Ingeniería MetalúrgicayQuímica Inorgánica, Universidad de Cádiz, Facultad de Ciencias, Apdo. 40, 11510, Puerto Real, Cádiz, Spain
| | - Apparao Draksharapu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christopher J Whiteoak
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Vlad Martin-Diaconescu
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Manuel G Basallote
- Departamento de Ciencia de los Materiales e Ingeniería MetalúrgicayQuímica Inorgánica, Universidad de Cádiz, Facultad de Ciencias, Apdo. 40, 11510, Puerto Real, Cádiz, Spain
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
| | - Anna Company
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain
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19
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Carr CE, Foster AW, Maroney MJ. An XAS investigation of the nickel site structure in the transcriptional regulator InrS. J Inorg Biochem 2017; 177:352-358. [PMID: 28844329 PMCID: PMC5741488 DOI: 10.1016/j.jinorgbio.2017.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/10/2017] [Accepted: 08/05/2017] [Indexed: 12/29/2022]
Abstract
InrS (Internal nickel-responsive Sensor) is a transcriptional repressor of the nickel exporter NrsD and de-represses expression of the exporter upon binding Ni(II) ions. Although a crystal structure of apo-InrS has been reported, no structure of the protein with metal ions bound is available. Herein we report the results of metal site structural investigations of Ni(II) and Cu(II) complexes of InrS using X-ray absorption spectroscopy (XAS) that are complementary to data available from the apo-InrS crystal structure, and are consistent with a planar four-coordinate [Ni(His)2(Cys)2] structure, where the ligands are derived from the side chains of His21, Cys53, His78, and Cys82. Coordination of Cu(II) to InrS forms a nearly identical planar four-coordinate complex that is consistent with a simple replacement of the Ni(II) center by Cu(II).
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Affiliation(s)
- Carolyn E Carr
- Chemistry Department, University of Massachusetts Amherst, MA 01003, USA
| | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK; Department of Chemistry, Durham University, Durham, UK
| | - Michael J Maroney
- Chemistry Department, University of Massachusetts Amherst, MA 01003, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, MA 01003, USA.
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20
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Muñoz-Escobar J, Kozlov G, Gehring K. Crystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding. Protein Sci 2017; 26:2092-2097. [PMID: 28691247 PMCID: PMC5606531 DOI: 10.1002/pro.3227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/02/2017] [Accepted: 07/03/2017] [Indexed: 11/06/2022]
Abstract
The UBR‐box is a 70‐residue zinc finger domain present in the UBR family of E3 ubiquitin ligases that directly binds N‐terminal degradation signals in substrate proteins. UBR6, also called FBXO11, is an UBR‐box containing E3 ubiquitin ligase that does not bind N‐terminal signals. Here, we present the crystal structure of the UBR‐box domain from human UBR6. The dimeric crystal structure reveals a unique form of domain swapping mediated by zinc coordination, where three independent protein chains come together to regenerate the topology of the monomeric UBR‐box fold. Analysis of the structure suggests that the absence of N‐terminal residue binding arises from the lack of an amino acid binding pocket. PDB Code(s): 5VMD
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Affiliation(s)
- Juliana Muñoz-Escobar
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, H3G0B1, Canada
| | - Guennadi Kozlov
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, H3G0B1, Canada
| | - Kalle Gehring
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, H3G0B1, Canada
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21
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Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ. Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR. Inorg Chem 2017; 56:6459-6476. [PMID: 28517938 DOI: 10.1021/acs.inorgchem.7b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli RcnR (resistance to cobalt and nickel regulator, EcRcnR) is a metal-responsive repressor of the genes encoding the Ni(II) and Co(II) exporter proteins RcnAB by binding to PRcnAB. The DNA binding affinity is weakened when the cognate ions Ni(II) and Co(II) bind to EcRcnR in a six-coordinate site that features a (N/O)5S ligand donor-atom set in distinct sites: while both metal ions are bound by the N terminus, Cys35, and His64, Co(II) is additionally bound by His3. On the other hand, the noncognate Zn(II) and Cu(I) ions feature a lower coordination number, have a solvent-accessible binding site, and coordinate protein ligands that do not include the N-terminal amine. A molecular model of apo-EcRcnR suggested potential roles for Glu34 and Glu63 in binding Ni(II) and Co(II) to EcRcnR. The roles of Glu34 and Glu63 in metal binding, metal selectivity, and function were therefore investigated using a structure/function approach. X-ray absorption spectroscopy was used to assess the structural changes in the Ni(II), Co(II), and Zn(II) binding sites of Glu → Ala and Glu → Cys variants at both positions. The effect of these structural alterations on the regulation of PrcnA by EcRcnR in response to metal binding was explored using LacZ reporter assays. These combined studies indicate that while Glu63 is a ligand for both metal ions, Glu34 is a ligand for Co(II) but possibly not for Ni(II). The Glu34 variants affect the structure of the cognate metal sites, but they have no effect on the transcriptional response. In contrast, the Glu63 variants affect both the structure and transcriptional response, although they do not completely abolish the function of EcRcnR. The structure of the Zn(II) site is not significantly perturbed by any of the glutamic acid variations. The spectroscopic and functional data obtained on the mutants were used to calculate models of the metal-site structures of EcRcnR bound to Ni(II), Co(II), and Zn(II). The results are interpreted in terms of a switch mechanism, in which a subset of the metal-binding ligands is responsible for the allosteric response required for DNA release.
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Affiliation(s)
- Carolyn E Carr
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University , Durham DH1 3LE, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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22
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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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23
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Hu HQ, Johnson RC, Merrell DS, Maroney MJ. Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori. Biochemistry 2017; 56:1105-1116. [PMID: 28177601 DOI: 10.1021/acs.biochem.6b00912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The human pathogen Helicobacter pylori requires nickel for colonization of the acidic environment of the stomach. HypA, a Ni metallochaperone that is typically associated with hydrogenase maturation, is also required for urease maturation and acid survival of H. pylori. There are two proposed Ni site structures for HypA; one is a paramagnetic six-coordinate site characterized by X-ray absorption spectroscopy (XAS) in unmodified HypA, while another is a diamagnetic four-coordinate planar site characterized by solution nuclear magnetic resonance in an N-terminally modified HypA construct. To determine the role of the N-terminal amine in Ni binding of HypA, an N-terminal extension variant, L2*-HypA, in which a leucine residue was inserted into the second position of the amino acid sequence in the proposed Ni-binding motif, was characterized in vitro and in vivo. Structural characterization of the Ni site using XAS showed a coordination change from six-coordinate in wild-type HypA (WT-HypA) to five-coordinate pyramidal in L2*-HypA, which was accompanied by the loss of two N/O donor protein ligands and the addition of an exogenous bromide ligand from the buffer. The magnetic properties of the Ni sites in WT-HypA compared to those of the Ni sites in L2*-HypA confirmed that a spin-state change from high to low spin accompanied this change in structure. The L2*-HypA H. pylori strain was shown to be acid sensitive and deficient in urease activity in vivo. In vitro characterization showed that L2*-HypA did not disrupt the HypA-UreE interaction that is essential for urease maturation but was at least 20-fold weaker in Ni binding than WT-HypA. Characterization of the L2*-HypA variant clearly demonstrates that the N-terminal amine of HypA is involved in proper Ni coordination and is necessary for urease activity and acid survival.
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Affiliation(s)
- Heidi Q Hu
- Department of Chemistry and Program of Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Ryan C Johnson
- Microbiology and Immunology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
| | - D Scott Merrell
- Microbiology and Immunology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
| | - Michael J Maroney
- Department of Chemistry and Program of Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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24
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Non-thiolate ligation of nickel by nucleotide-free UreG of Klebsiella aerogenes. J Biol Inorg Chem 2016; 22:497-503. [PMID: 28004186 DOI: 10.1007/s00775-016-1429-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
Abstract
Nickel-dependent ureases are activated by a multiprotein complex that includes the GTPase UreG. Prior studies showed that nucleotide-free UreG from Klebsiella aerogenes is monomeric and binds one nickel or zinc ion with near-equivalent affinity using an undefined binding site, whereas nucleotide-free UreG from Helicobacter pylori selectively binds one zinc ion per dimer via a universally conserved Cys-Pro-His motif in each protomer. Iodoacetamide-treated K. aerogenes UreG was nearly unaffected in nickel binding compared to non-treated sample, suggesting the absence of thiolate ligands to the metal. X-ray absorption spectroscopy of nickel-bound UreG showed the metal possessed four-coordinate geometry with all O/N donor ligands including one imidazole, thus confirming the absence of thiolate ligation. The nickel site in Strep-tag II-modified protein possessed six-coordinate geometry, again with all O/N donor ligands, but now including two or three imidazoles. An identical site was noted for the Strep-tag II-modified H74A variant, substituted in the Cys-Pro-His motif, ruling out coordination by this His residue. These results are consistent with metal binding to both His6 and a His residue of the fusion peptide in Strep-tagged K. aerogenes UreG. We conclude that the nickel- and zinc-binding site in nucleotide-free K. aerogenes UreG is distinct from that of nucleotide-free H. pylori UreG and does not involve the Cys-Pro-His motif. Further, we show the Strep-tag II can perturb metal coordination of this protein.
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25
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Corona T, Draksharapu A, Padamati SK, Gamba I, Martin-Diaconescu V, Acuña-Parés F, Browne WR, Company A. Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel-Oxygen Species. J Am Chem Soc 2016; 138:12987-12996. [PMID: 27598293 DOI: 10.1021/jacs.6b07544] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Terminal high-valent metal-oxygen species are key reaction intermediates in the catalytic cycle of both enzymes (e.g., oxygenases) and synthetic oxidation catalysts. While tremendous efforts have been directed toward the characterization of the biologically relevant terminal manganese-oxygen and iron-oxygen species, the corresponding analogues based on late-transition metals such as cobalt, nickel or copper are relatively scarce. This scarcity is in part related to the "Oxo Wall" concept, which predicts that late transition metals cannot support a terminal oxido ligand in a tetragonal environment. Here, the nickel(II) complex (1) of the tetradentate macrocyclic ligand bearing a 2,6-pyridinedicarboxamidate unit is shown to be an effective catalyst in the chlorination and oxidation of C-H bonds with sodium hypochlorite as terminal oxidant in the presence of acetic acid (AcOH). Insight into the active species responsible for the observed reactivity was gained through the study of the reaction of 1 with ClO- at low temperature by UV-vis absorption, resonance Raman, EPR, ESI-MS, and XAS analyses. DFT calculations aided the assignment of the trapped chromophoric species (3) as a nickel-hypochlorite species. Despite the fact that the formal oxidation state of the nickel in 3 is +4, experimental and computational analysis indicate that 3 is best formulated as a NiIII complex with one unpaired electron delocalized in the ligands surrounding the metal center. Most remarkably, 3 reacts rapidly with a range of substrates including those with strong aliphatic C-H bonds, indicating the direct involvement of 3 in the oxidation/chlorination reactions observed in the 1/ClO-/AcOH catalytic system.
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Affiliation(s)
- Teresa Corona
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 69 , E17003 Girona, Catalonia, Spain
| | - Apparao Draksharapu
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sandeep K Padamati
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ilaria Gamba
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 69 , E17003 Girona, Catalonia, Spain
| | - Vlad Martin-Diaconescu
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 69 , E17003 Girona, Catalonia, Spain
| | - Ferran Acuña-Parés
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 69 , E17003 Girona, Catalonia, Spain
| | - Wesley R Browne
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna Company
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 69 , E17003 Girona, Catalonia, Spain
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26
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Amartely H, David A, Shamir M, Lebendiker M, Izraeli S, Friedler A. Differential effects of zinc binding on structured and disordered regions in the multidomain STIL protein. Chem Sci 2016; 7:4140-4147. [PMID: 30155058 PMCID: PMC6014068 DOI: 10.1039/c6sc00115g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/01/2016] [Indexed: 11/24/2022] Open
Abstract
Here we show that simultaneous binding of Zn2+ ions has different effects on structured and disordered domains in the same multidomain protein.
Binding of metal ions is an important regulatory mechanism in proteins. Specifically, Zn2+ binding to disordered regions commonly induces a disorder to order transition and gain of structure or oligomerization. Here we show that simultaneous binding of Zn2+ ions has different effects on structured and disordered domains in the same multidomain protein. The centrosomal STIL protein bound Zn2+ ions via both its structured N-terminal domain (NTD) and disordered central region (IDR). Zn2+ binding induced structural rearrangement of the structured NTD but promoted oligomerization of the IDR. We suggest that by binding Zn2+ STIL acquires a different conformation, which allows its oligomerization and induces its activity. Sequence alignment of the oligomerization region revealed a new suggested motif, SxKxS/SxHxS/SxLxS, which may participate in STIL oligomerization. Binding of the same metal ion through a disordered and a structured domain in the same protein is a property that may have implications in regulating the protein activity. By doing so, the protein achieves two parallel outcomes: structural changes and oligomerization that can take place together. Our results describe a new important role of the delicate interplay between structure and intrinsic disorder in proteins.
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Affiliation(s)
- Hadar Amartely
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Ahuvit David
- Sheba Cancer Research Center and the Edmond and Lily Safra Children Hospital , Sheba Medical Center , Tel-Hashomer 52621 , Israel.,Department of Molecular Genetics and Biochemistry , Faculty of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Mai Shamir
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Shai Izraeli
- Sheba Cancer Research Center and the Edmond and Lily Safra Children Hospital , Sheba Medical Center , Tel-Hashomer 52621 , Israel.,Department of Molecular Genetics and Biochemistry , Faculty of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Assaf Friedler
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
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27
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28
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Corona T, Pfaff FF, Acuña-Parés F, Draksharapu A, Whiteoak CJ, Martin-Diaconescu V, Lloret-Fillol J, Browne WR, Ray K, Company A. Reactivity of a Nickel(II) Bis(amidate) Complex with meta-Chloroperbenzoic Acid: Formation of a Potent Oxidizing Species. Chemistry 2015; 21:15029-38. [PMID: 26311073 DOI: 10.1002/chem.201501841] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Herein, we report the formation of a highly reactive nickel-oxygen species that has been trapped following reaction of a Ni(II) precursor bearing a macrocyclic bis(amidate) ligand with meta-chloroperbenzoic acid (HmCPBA). This compound is only detectable at temperatures below 250 K and is much more reactive toward organic substrates (i.e., C-H bonds, C=C bonds, and sulfides) than previously reported well-defined nickel-oxygen species. Remarkably, this species is formed by heterolytic O-O bond cleavage of a Ni-HmCPBA precursor, which is concluded from experimental and computational data. On the basis of spectroscopy and DFT calculations, this reactive species is proposed to be a Ni(III) -oxyl compound.
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Affiliation(s)
- Teresa Corona
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Florian F Pfaff
- Humboldt Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, 12489 Berlin (Germany)
| | - Ferran Acuña-Parés
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Apparao Draksharapu
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Christopher J Whiteoak
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Vlad Martin-Diaconescu
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Julio Lloret-Fillol
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50.,Current address: Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona (Spain)
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Kallol Ray
- Humboldt Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, 12489 Berlin (Germany)
| | - Anna Company
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50.
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29
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Musiani F, Ciurli S. Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria. Molecules 2015; 20:14265-92. [PMID: 26251891 PMCID: PMC6332059 DOI: 10.3390/molecules200814265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022] Open
Abstract
The interaction between macromolecules is a fundamental aspect of most biological processes. The computational techniques used to study protein-protein and protein-nucleic acid interactions have evolved in the last few years because of the development of new algorithms that allow the a priori incorporation, in the docking process, of experimentally derived information, together with the possibility of accounting for the flexibility of the interacting molecules. Here we review the results and the evolution of the techniques used to study the interaction between metallo-proteins and DNA operators, all involved in the nickel and iron metabolism of pathogenic bacteria, focusing in particular on Helicobacter pylori (Hp). In the first part of the article we discuss the methods used to calculate the structure of complexes of proteins involved in the activation of the nickel-dependent enzyme urease. In the second part of the article, we concentrate on two applications of protein-DNA docking conducted on the transcription factors HpFur (ferric uptake regulator) and HpNikR (nickel regulator). In both cases we discuss the technical expedients used to take into account the conformational variability of the multi-domain proteins involved in the calculations.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
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30
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Yang X, Li H, Cheng T, Xia W, Lai YT, Sun H. Nickel translocation between metallochaperones HypA and UreE in Helicobacter pylori. Metallomics 2015; 6:1731-6. [PMID: 25010720 DOI: 10.1039/c4mt00134f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Incorporation of nickel ions to the active sites of urease and hydrogenase is prerequisite for the appropriate functions of the metalloenzymes. Such a process requires the participation of several accessory proteins. Interestingly, some of them are shared by the two enzymes in their maturation processes. In this work, we characterized the molecular details of the interaction of metallochaperones UreE and HypA in Helicobacter pylori. We show by chemical cross-linking and static light scattering that the UreE dimer binds to HypA to form a hetero-complex i.e. HypA-(UreE)2. The dissociation constant (Kd) of the protein complex was determined by ITC to be 1 μM in the absence of nickel ions; whereas binding of Ni(2+) but not Zn(2+) to UreE resulted in ca. one fold decrease in the affinity. The putative interfaces on HypA unveiled by NMR chemical shift perturbation were found mainly at the nickel binding domain and in the cleft between α1 and β1/β6. We also identified that the C-domain of UreE, in particular the C-terminal residues of 158-170 are indispensable for the interaction of UreE and HypA. Such an interaction was also observed intracellularly by GFP-fragment reassembly assay. Moreover, we demonstrated using a fluorescent probe that nickel is transferred from HypA to UreE via the specific protein-protein interaction. Deletion of the C-terminus (residues 158-170) of UreE abolished nickel transfer and led to a significant decrease in urease activity. This study provides direct in vitro and in vivo evidence as well as molecular details of nickel translocation mediated by protein-protein interaction.
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Affiliation(s)
- Xinming Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China.
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31
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Miraula M, Ciurli S, Zambelli B. Intrinsic disorder and metal binding in UreG proteins from Archae hyperthermophiles: GTPase enzymes involved in the activation of Ni(II) dependent urease. J Biol Inorg Chem 2015; 20:739-55. [PMID: 25846143 DOI: 10.1007/s00775-015-1261-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/20/2015] [Indexed: 02/03/2023]
Abstract
Urease is a Ni(II) enzyme present in every domain of life, in charge for nitrogen recycling through urea hydrolysis. Its activity requires the presence of two Ni(II) ions in the active site. These are delivered by the concerted action of four accessory proteins, named UreD, UreF, UreG and UreE. This process requires protein flexibility at different levels and some disorder-to-order transition events that coordinate the mechanism of protein-protein interaction. In particular, UreG, the GTPase in charge of nucleotide hydrolysis required for urease activation, presents a significant degree of intrinsic disorder, existing as a conformational ensemble featuring characteristics that recall a molten globule. Here, the folding properties of UreG were explored in Archaea hyperthermophiles, known to generally feature significantly low level of structural disorder in their proteome. UreG proteins from Methanocaldococcus jannaschii (Mj) and Metallosphaera sedula (Ms) were structurally and functionally analyzed by integrating circular dichroism, NMR, light scattering and enzymatic assays. Metal-binding properties were studied using isothermal titration calorimetry. The results indicate that, as the mesophilic counterparts, both proteins contain a significant amount of secondary structure but maintain a flexible fold and a low GTPase activity. As opposed to other UreGs, secondary structure is lost at high temperatures (68 and 75 °C, respectively) with an apparent two-state mechanism. Both proteins bind Zn(II) and Ni(II), with affinities two orders of magnitude higher for Zn(II) than for Ni(II). No major modifications of the average conformational ensemble are observed, but binding of Zn(II) yields a more compact dimeric form in MsUreG.
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Affiliation(s)
- Manfredi Miraula
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
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32
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Yang X, Li H, Lai TP, Sun H. UreE-UreG complex facilitates nickel transfer and preactivates GTPase of UreG in Helicobacter pylori. J Biol Chem 2015; 290:12474-85. [PMID: 25752610 DOI: 10.1074/jbc.m114.632364] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 11/06/2022] Open
Abstract
The pathogenicity of Helicobacter pylori relies heavily on urease, which converts urea to ammonia to neutralize the stomach acid. Incorporation of Ni(2+) into the active site of urease requires a battery of chaperones. Both metallochaperones UreE and UreG play important roles in the urease activation. In this study, we demonstrate that, in the presence of GTP and Mg(2+), UreG binds Ni(2+) with an affinity (Kd) of ∼0.36 μm. The GTPase activity of Ni(2+)-UreG is stimulated by both K(+) (or NH4 (+)) and HCO3 (-) to a biologically relevant level, suggesting that K(+)/NH4 (+) and HCO3 (-) might serve as GTPase elements of UreG. We show that complexation of UreE and UreG results in two protein complexes, i.e. 2E-2G and 2E-G, with the former being formed only in the presence of both GTP and Mg(2+). Mutagenesis studies reveal that Arg-101 on UreE and Cys-66 on UreG are critical for stabilization of 2E-2G complex. Combined biophysical and bioassay studies show that the formation of 2E-2G complex not only facilitates nickel transfer from UreE to UreG, but also enhances the binding of GTP. This suggests that UreE might also serve as a structural scaffold for recruitment of GTP to UreG. Importantly, we demonstrate for the first time that UreE serves as a bridge to grasp Ni(2+) from HypA, subsequently donating it to UreG. The study expands our horizons on the molecular details of nickel translocation among metallochaperones UreE, UreG, and HypA, which further extends our knowledge on the urease maturation process.
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Affiliation(s)
- Xinming Yang
- From the Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Li
- From the Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tsz-Pui Lai
- From the Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongzhe Sun
- From the Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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33
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Martin-Diaconescu V, Gennari M, Gerey B, Tsui E, Kanady J, Tran R, Pécaut J, Maganas D, Krewald V, Gouré E, Duboc C, Yano J, Agapie T, Collomb MN, DeBeer S. Ca K-edge XAS as a probe of calcium centers in complex systems. Inorg Chem 2015; 54:1283-92. [PMID: 25492398 PMCID: PMC4331723 DOI: 10.1021/ic501991e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 12/21/2022]
Abstract
Herein, Ca K-edge X-ray absorption spectroscopy (XAS) is developed as a means to characterize the local environment of calcium centers. The spectra for six, seven, and eight coordinate inorganic and molecular calcium complexes were analyzed and determined to be primarily influenced by the coordination environment and site symmetry at the calcium center. The experimental results are closely correlated to time-dependent density functional theory (TD-DFT) calculations of the XAS spectra. The applicability of this methodology to complex systems was investigated using structural mimics of the oxygen-evolving complex (OEC) of PSII. It was found that Ca K-edge XAS is a sensitive probe for structural changes occurring in the cubane heterometallic cluster due to Mn oxidation. Future applications to the OEC are discussed.
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Affiliation(s)
- Vlad Martin-Diaconescu
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Marcello Gennari
- Univ. Grenoble Alpes, DCM and
CNRS, DCM, F-38000 Grenoble, France
| | - Bertrand Gerey
- Univ. Grenoble Alpes, DCM and
CNRS, DCM, F-38000 Grenoble, France
| | - Emily Tsui
- California Institute of
Technology, Department of Chemistry, Pasadena, California 91125, United States
| | - Jacob Kanady
- California Institute of
Technology, Department of Chemistry, Pasadena, California 91125, United States
| | - Rosalie Tran
- Lawrence Berkeley National Laboratory − Physical Biosciences Division, Berkeley, California 94720, United States
| | - Jacques Pécaut
- Laboratoire de Reconnaissance Ionique
et Chimie de Coordination (LCIB, SCIB, INAC, CEA Grenoble), 38054 Grenoble
Cedex 9, France
| | - Dimitrios Maganas
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Vera Krewald
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eric Gouré
- Univ. Grenoble Alpes, DCM and
CNRS, DCM, F-38000 Grenoble, France
| | - Carole Duboc
- Univ. Grenoble Alpes, DCM and
CNRS, DCM, F-38000 Grenoble, France
| | - Junko Yano
- Lawrence Berkeley National Laboratory − Physical Biosciences Division, Berkeley, California 94720, United States
| | - Theodor Agapie
- California Institute of
Technology, Department of Chemistry, Pasadena, California 91125, United States
| | | | - Serena DeBeer
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical
Biology, Cornell University, Ithaca, New York 14853, United States
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34
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Merloni A, Dobrovolska O, Zambelli B, Agostini F, Bazzani M, Musiani F, Ciurli S. Molecular landscape of the interaction between the urease accessory proteins UreE and UreG. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1662-74. [PMID: 24982029 DOI: 10.1016/j.bbapap.2014.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/12/2014] [Accepted: 06/19/2014] [Indexed: 01/07/2023]
Abstract
Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9μM; Kd2=1.7±0.3μM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed.
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Affiliation(s)
- Anna Merloni
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Olena Dobrovolska
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Federico Agostini
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Micaela Bazzani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.
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35
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Dong J, Joseph CA, Borotto NB, Gill V, Maroney MJ, Vachet RW. Unique effect of Cu(II) in the metal-induced amyloid formation of β-2-microglobulin. Biochemistry 2014; 53:1263-74. [PMID: 24450572 PMCID: PMC3985682 DOI: 10.1021/bi4016583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/12/2014] [Indexed: 01/14/2023]
Abstract
β-2-Microglobulin (β2m) forms amyloid fibrils in the joints of patients undergoing hemodialysis treatment as a result of kidney failure. In the presence of stoichiometric amounts of Cu(II), β2m self-associates into discrete oligomeric species, including dimers, tetramers, and hexamers, before ultimately forming amyloid fibrils that contain no copper. To improve our understanding of whether Cu(II) is unique in its ability to induce β2m amyloid formation and to delineate the coordinative interactions that allow Cu(II) to exert its effect, we have examined the binding of Ni(II) and Zn(II) to β2m and the resulting influence that these metals have on β2m aggregation. We find that, in contrast to Cu(II), Ni(II) does not induce the oligomerization or aggregation of β2m, while Zn(II) promotes oligomerization but not amyloid fibril formation. Using X-ray absorption spectroscopy and new mass spectrometry-related techniques, we find that different binding modes are responsible for the different effects of Ni(II) and Zn(II). By comparing the binding modes of Cu(II) with Ni(II), we find that Cu(II) binding to Asp59 and the backbone amide between the first two residues of β2m are important for allowing the formation of amyloid-competent oligomers, as Ni(II) appears not to bind these sites on the protein. The oligomers formed in the presence of Zn(II) are permitted by this metal's ability to bridge two β2m units via His51. These oligomers, however, are not able to progress to form amyloid fibrils because Zn(II) does not induce the required structural changes near the N-terminus and His31.
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Affiliation(s)
- Jia Dong
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Crisjoe A. Joseph
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Nicholas B. Borotto
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Vanessa
L. Gill
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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36
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Zambelli B, Berardi A, Martin-Diaconescu V, Mazzei L, Musiani F, Maroney MJ, Ciurli S. Nickel binding properties of Helicobacter pylori UreF, an accessory protein in the nickel-based activation of urease. J Biol Inorg Chem 2014; 19:319-34. [PMID: 24292245 PMCID: PMC3943961 DOI: 10.1007/s00775-013-1068-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/14/2013] [Indexed: 02/08/2023]
Abstract
Helicobacter pylori UreF (HpUreF) is involved in the insertion of Ni(2+) in the urease active site. The recombinant protein in solution is a dimer characterized by an extensive α-helical structure and a well-folded tertiary structure. HpUreF binds two Ni(2+) ions per dimer, with a micromolar dissociation constant, as shown by calorimetry. X-ray absorption spectroscopy indicated that the Ni(2+) ions reside in a five-coordinate pyramidal geometry comprising exclusively N/O-donor ligands derived from the protein, including one or two histidine imidazole and carboxylate ligands. Binding of Ni(2+) does not affect the solution properties of the protein. Mutation to alanine of His229 and/or Cys231, a pair of residues located on the protein surface that interact with H. pylori UreD, altered the affinity of the protein for Ni(2+). This result, complemented by the findings from X-ray absorption spectroscopy, indicates that the Ni(2+) binding site involves His229, and that Cys231 has an indirect structural role in metal binding. An in vivo assay of urease activation demonstrated that H229A HpUreF, C231A HpUreF, and H229/C231 HpUreF are significantly less competent in this process, suggesting a role for a Ni(2+) complex with UreF in urease maturation. This hypothesis was supported by calculations revealing the presence of a tunnel that joins the Cys-Pro-His metal binding site on UreG and an opening on the UreD surface, passing through UreF close to His229 and Cys231, in the structure of the H. pylori UreDFG complex. This tunnel could be used to transfer nickel into the urease active site during apoenzyme-to-holoenzyme activation.
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Affiliation(s)
- Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna (Italy)
| | - Andrea Berardi
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna (Italy)
| | | | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna (Italy)
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna (Italy)
- International School for Advanced Studies (Sissa/ISAS), Trieste (Italy)
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst 01003, MA, USA
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna (Italy)
- Center for Magnetic Resonance (CERM), University of Florence (Italy)
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Rowinska-Zyrek M, Zakrzewska-Czerwinska J, Zawilak-Pawlik A, Kozlowski H. Ni2+chemistry in pathogens – a possible target for eradication. Dalton Trans 2014; 43:8976-89. [DOI: 10.1039/c4dt00421c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel homeostasis inHelicobacter pyloriand potential histidine-rich binding sites from various bacterial and fungal pathogens are discussed.
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Affiliation(s)
| | - Jolanta Zakrzewska-Czerwinska
- Faculty of Biotechnology
- University of Wroclaw
- 50-383 Wroclaw, Poland
- Institute of Immunology and Experimental Therapy
- Polish Academy of Sciences
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy
- Polish Academy of Sciences
- Department of Microbiology
- 53-114 Wrocław, Poland
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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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Selectivity of Ni(II) and Zn(II) binding to Sporosarcina pasteurii UreE, a metallochaperone in the urease assembly: a calorimetric and crystallographic study. J Biol Inorg Chem 2013; 18:1005-17. [PMID: 24126709 DOI: 10.1007/s00775-013-1049-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/13/2013] [Indexed: 10/26/2022]
Abstract
Urease is a nickel-dependent enzyme that plays a critical role in the biogeochemical nitrogen cycle by catalyzing the hydrolysis of urea to ammonia and carbamate. This enzyme, initially synthesized in the apo form, needs to be activated by incorporation of two nickel ions into the active site, a process driven by the dimeric metallochaperone UreE. Previous studies reported that this protein can bind different metal ions in vitro, beside the cognate Ni(II). This study explores the metal selectivity and affinity of UreE from Sporosarcina pasteurii (Sp, formerly known as Bacillus pasteurii) for cognate [Ni(II)] and noncognate [Zn(II)] metal ions. In particular, the thermodynamic parameters of SpUreE Ni(II) and Zn(II) binding have been determined using isothermal titration calorimetry. These experiments show that two Ni(II) ions bind to the protein dimer with positive cooperativity. The high-affinity site involves the conserved solvent-exposed His(100) and the C-terminal His(145), whereas the low-affinity site comprises also the C-terminal His(147). Zn(II) binding to the protein, occurring in the same protein regions and with similar affinity as compared to Ni(II), causes metal-driven dimerization of the protein dimer. The crystal structure of the protein obtained in the presence of equimolar amounts of both metal ions indicates that the high-affinity metal binding site binds Ni(II) preferentially over Zn(II). The ability of the protein to select Ni(II) over Zn(II) was confirmed by competition experiments in solution as well as by analysis of X-ray anomalous dispersion data. Overall, the thermodynamics and structural parameters that modulate the metal ion specificity of the different binding sites on the protein surface of SpUreE have been established.
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Structure of UreG/UreF/UreH complex reveals how urease accessory proteins facilitate maturation of Helicobacter pylori urease. PLoS Biol 2013; 11:e1001678. [PMID: 24115911 PMCID: PMC3792862 DOI: 10.1371/journal.pbio.1001678] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Structural and biochemical study of urease accessory protein complex provides mechanistic insights into the delivery of nickel to metalloenzyme urease, an enzyme enabling the survival of Helicobacter pylori in the human stomach. Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. Catalytic activities of many important enzymes depend upon metal cofactors. Ensuring each enzyme acquires the proper type of metal cofactor is essential to life. One such example is urease, which is a nickel containing metalloenzyme catalyzing the hydrolysis of urea to ammonia. The survival of Helicobacter pylori, a stomach ulcer–causing pathogen, in the human stomach depends on the ammonia released to neutralize gastric acid. In this study, we revealed the detail mechanism of how urease accessory proteins UreF, UreH, and UreG cooperate to couple GTP hydrolysis to deliver nickel to urease. UreF/UreH complex interacts with two molecules of GTPase UreG and assembles a metal binding site located at the interface between two UreG molecules. Nickel can induce GTP-dependent dimerization of UreG. This nickel-carrying UreG dimer together with UreF, UreH, and urease assemble into a protein complex. Upon stimulation of UreG GTPase activity by bicarbonate, UreG hydrolyses GTP and releases nickel into urease. Other nickel-delivering NTPases share similar properties with UreG; therefore, the nickel delivery mechanism described here is likely universally shared among these proteins.
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Structure of the UreD-UreF-UreG-UreE complex in Helicobacter pylori: a model study. J Biol Inorg Chem 2013; 18:571-7. [PMID: 23661161 DOI: 10.1007/s00775-013-1002-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
The molecular details of the protein complex formed by UreD, UreF, UreG, and UreE, accessory proteins for urease activation in the carcinogenic bacterium Helicobacter pylori, have been elucidated using computational modeling. The calculated structure of the complex supports the hypothesis of UreF acting as a GTPase activation protein that facilitates GTP hydrolysis by UreG during urease maturation, and provides a rationale for the design of new drugs against infections by ureolytic bacterial pathogens.
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Abstract
Metalloenzymes often require elaborate metallocenter assembly systems to create functional active sites. The medically important dinuclear nickel enzyme urease provides an excellent model for studying metallocenter assembly. Nickel is inserted into the urease active site in a GTP-dependent process with the assistance of UreD/UreH, UreE, UreF, and UreG. These accessory proteins orchestrate apoprotein activation by delivering the appropriate metal, facilitating protein conformational changes, and possibly providing a requisite post-translational modification. The activation mechanism and roles of each accessory protein in urease maturation are the subject of ongoing studies, with the latest findings presented in this minireview.
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Affiliation(s)
- Mark A Farrugia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Abstract
This review focuses on the impact of nickel on human health. In particular, the dual nature of nickel as an essential as well as toxic element in nature is described, and the main forms of nickel that can come in contact with living systems from natural sources and anthropogenic activities are discussed. Concomitantly, the main routes of nickel uptake and transport in humans are covered, and the potential dangers that nickel exposure can represent for health are described. In particular, the insurgence of nickel-derived allergies, nickel-induced carcinogenesis as well as infectious diseases caused by human pathogens that rely on nickel-based enzymes to colonize the host are reviewed at different levels, from their macroscopic aspects on human health to the molecular mechanisms underlying these points. Finally, the importance of nickel as a beneficial element for human health, especially being essential for microorganisms that colonize the human guts, is examined.
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Affiliation(s)
- Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy,
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Higgins KA, Carr CE, Maroney MJ. Specific metal recognition in nickel trafficking. Biochemistry 2012; 51:7816-32. [PMID: 22970729 DOI: 10.1021/bi300981m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. As with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. Because there are few enzymes (targets) that require nickel for activity (e.g., Escherichia coli transports nickel for hydrogenases made under anaerobic conditions, and Helicobacter pylori requires nickel for hydrogenase and urease that are essential for acid viability), the "traffic pattern" for nickel is relatively simple, and nickel trafficking therefore presents an opportunity to examine a system for the mechanisms that are used to distinguish nickel from other metals. In this review, we describe the details known for examples of uptake permeases, metallochaperones and proteins involved in metallocenter assembly, and nickel metalloregulators. We also illustrate a variety of mechanisms, including molecular recognition in the case of NikA protein and examples of allosteric regulation for HypA, NikR, and RcnR, employed to generate specific biological responses to nickel ions.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Benoit SL, McMurry JL, Hill SA, Maier RJ. Helicobacter pylori hydrogenase accessory protein HypA and urease accessory protein UreG compete with each other for UreE recognition. Biochim Biophys Acta Gen Subj 2012; 1820:1519-25. [PMID: 22698670 DOI: 10.1016/j.bbagen.2012.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 01/15/2023]
Abstract
BACKGROUND The gastric pathogen Helicobacter pylori relies on nickel-containing urease and hydrogenase enzymes in order to colonize the host. Incorporation of Ni(2+) into urease is essential for the function of the enzyme and requires the action of several accessory proteins, including the hydrogenase accessory proteins HypA and HypB and the urease accessory proteins UreE, UreF, UreG and UreH. METHODS Optical biosensing methods (biolayer interferometry and plasmon surface resonance) were used to screen for interactions between HypA, HypB, UreE and UreG. RESULTS Using both methods, affinity constants were found to be 5nM and 13nM for HypA-UreE and 8μM and 14μM for UreG-UreE. Neither Zn(2+) nor Ni(2+) had an effect on the kinetics or stability of the HypA-UreE complex. By contrast, addition of Zn(2+), but not Ni(2+), altered the kinetics and greatly increased the stability of the UreE-UreG complex, likely due in part to Zn(2+)-mediated oligomerization of UreE. Finally our results unambiguously show that HypA, UreE and UreG cannot form a heterotrimeric protein complex in vitro; instead, HypA and UreG compete with each other for UreE recognition. GENERAL SIGNIFICANCE Factors influencing the pathogen's nickel budget are important to understand pathogenesis and for future drug design.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, 805 Biological Sciences Bldg., Athens, GA, USA
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