1
|
Osterberg MK, Smith AK, Campbell C, Deredge DJ, Stemmler TL, Giedroc DP. Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA. Biophys J 2024; 123:979-991. [PMID: 38459695 PMCID: PMC11052692 DOI: 10.1016/j.bpj.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
COG0523 proteins, also known as nucleotide-dependent metallochaperones, are a poorly understood class of small P-loop G3E GTPases. Multiple family members play critical roles in bacterial pathogen survival during an infection as part of the adaptive response to host-mediated "nutritional immunity." Our understanding of the structure, dynamics, and molecular-level function of COG0523 proteins, apart from the eukaryotic homolog, Zng1, remains in its infancy. Here, we use X-ray absorption spectroscopy to establish that Acinetobacter baumannii (Ab) ZigA coordinates ZnII using all three cysteines derived from the invariant CXCC motif to form an S3(N/O) coordination complex, a feature inconsistent with the ZnII-bound crystal structure of a distantly related COG0523 protein of unknown function from Escherichia coli, EcYjiA. The binding of ZnII and guanine nucleotides is thermodynamically linked in AbZigA, and this linkage is more favorable for the substrate GTP relative to the product GDP. Part of this coupling originates with nucleotide-induced stabilization of the G-domain tertiary structure as revealed by global thermodynamics measurements and hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS also reveals that the HDX behavior of the G2 (switch 1) loop is highly sensitive to nucleotide status and becomes more exchange labile in the GDP (product)-bound state. Significant long-range perturbation of local stability in both the G-domain and the C-terminal domain define a candidate binding pocket for a client protein that appears sensitive to nucleotide status (GDP versus GTP). We place these new insights into the structure, dynamics, and energetics of intermolecular metal transfer into the context of a model for AbZigA metallochaperone function.
Collapse
Affiliation(s)
| | - Ally K Smith
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Courtney Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana.
| |
Collapse
|
2
|
Korf L, Ye X, Vogt MS, Steinchen W, Watad M, van der Does C, Tourte M, Sivabalasarma S, Albers SV, Essen LO. Archaeal GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis. mBio 2023; 14:e0085923. [PMID: 37962382 PMCID: PMC10746158 DOI: 10.1128/mbio.00859-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/05/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE GPN-loop GTPases have been found to be crucial for eukaryotic RNA polymerase II assembly and nuclear trafficking. Despite their ubiquitous occurrence in eukaryotes and archaea, the mechanism by which these GTPases mediate their function is unknown. Our study on an archaeal representative from Sulfolobus acidocaldarius showed that these dimeric GTPases undergo large-scale conformational changes upon GTP hydrolysis, which can be summarized as a lock-switch-rock mechanism. The observed requirement of SaGPN for motility appears to be due to its large footprint on the archaeal proteome.
Collapse
Affiliation(s)
- Lukas Korf
- Department of Chemistry, Philipps University, Marburg, Germany
| | - Xing Ye
- University of Freiburg, Institute of Biology, Molecular Biology of Archaea, Freiburg, Germany
| | - Marian S. Vogt
- Department of Chemistry, Philipps University, Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, Philipps University, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Strasse, Marburg, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University, Marburg, Germany
| | - Chris van der Does
- University of Freiburg, Institute of Biology, Molecular Biology of Archaea, Freiburg, Germany
| | - Maxime Tourte
- University of Freiburg, Institute of Biology, Molecular Biology of Archaea, Freiburg, Germany
| | - Shamphavi Sivabalasarma
- University of Freiburg, Institute of Biology, Molecular Biology of Archaea, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- University of Freiburg, Institute of Biology, Molecular Biology of Archaea, Freiburg, Germany
| | | |
Collapse
|
3
|
Vaccaro FA, Faber DA, Andree GA, Born DA, Kang G, Fonseca DR, Jost M, Drennan CL. Structural insight into G-protein chaperone-mediated maturation of a bacterial adenosylcobalamin-dependent mutase. J Biol Chem 2023; 299:105109. [PMID: 37517695 PMCID: PMC10481361 DOI: 10.1016/j.jbc.2023.105109] [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: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
G-protein metallochaperones are essential for the proper maturation of numerous metalloenzymes. The G-protein chaperone MMAA in humans (MeaB in bacteria) uses GTP hydrolysis to facilitate the delivery of adenosylcobalamin (AdoCbl) to AdoCbl-dependent methylmalonyl-CoA mutase, an essential metabolic enzyme. This G-protein chaperone also facilitates the removal of damaged cobalamin (Cbl) for repair. Although most chaperones are standalone proteins, isobutyryl-CoA mutase fused (IcmF) has a G-protein domain covalently attached to its target mutase. We previously showed that dimeric MeaB undergoes a 180° rotation to reach a state capable of GTP hydrolysis (an active G-protein state), in which so-called switch III residues of one protomer contact the G-nucleotide of the other protomer. However, it was unclear whether other G-protein chaperones also adopted this conformation. Here, we show that the G-protein domain in a fused system forms a similar active conformation, requiring IcmF oligomerization. IcmF oligomerizes both upon Cbl damage and in the presence of the nonhydrolyzable GTP analog, guanosine-5'-[(β,γ)-methyleno]triphosphate, forming supramolecular complexes observable by mass photometry and EM. Cryo-EM structural analysis reveals that the second protomer of the G-protein intermolecular dimer props open the mutase active site using residues of switch III as a wedge, allowing for AdoCbl insertion or damaged Cbl removal. With the series of structural snapshots now available, we now describe here the molecular basis of G-protein-assisted AdoCbl-dependent mutase maturation, explaining how GTP binding prepares a mutase for cofactor delivery and how GTP hydrolysis allows the mutase to capture the cofactor.
Collapse
Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daphne A Faber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gisele A Andree
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David A Born
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dallas R Fonseca
- Amgen Scholar Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| |
Collapse
|
4
|
Mascarenhas R, Ruetz M, Gouda H, Heitman N, Yaw M, Banerjee R. Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. Nat Commun 2023; 14:4332. [PMID: 37468522 PMCID: PMC10356863 DOI: 10.1038/s41467-023-40077-4] [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: 04/22/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B12-dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.
Collapse
Affiliation(s)
- Romila Mascarenhas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Markus Ruetz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Harsha Gouda
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natalie Heitman
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline Yaw
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
5
|
Mascarenhas R, Ruetz M, Gouda H, Heitman N, Yaw M, Banerjee R. Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533963. [PMID: 36993209 PMCID: PMC10055420 DOI: 10.1101/2023.03.23.533963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. MMAA, a G-protein motor, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B 12 -dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the motor assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nanomotor assembly, which reveals a dramatic 180° rotation of the B 12 domain, exposing it to solvent. The nanomotor complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the newly identified MMAA-MMUT interfaces.
Collapse
|
6
|
Vaccaro FA, Drennan CL. The role of nucleoside triphosphate hydrolase metallochaperones in making metalloenzymes. Metallomics 2022; 14:6575898. [PMID: 35485745 PMCID: PMC9164220 DOI: 10.1093/mtomcs/mfac030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022]
Abstract
Metalloenzymes catalyze a diverse set of challenging chemical reactions that are essential for life. These metalloenzymes rely on a wide range of metallocofactors, from single metal ions to complicated metallic clusters. Incorporation of metal ions and metallocofactors into apo-proteins often requires the assistance of proteins known as metallochaperones. Nucleoside triphosphate hydrolases (NTPases) are one important class of metallochaperones and are found widely distributed throughout the domains of life. These proteins use the binding and hydrolysis of nucleoside triphosphates, either adenosine triphosphate (ATP) or guanosine triphosphate (GTP), to carry out highly specific and regulated roles in the process of metalloenzyme maturation. Here, we review recent literature on NTPase metallochaperones and describe the current mechanistic proposals and available structural data. By using representative examples from each type of NTPase, we also illustrate the challenges in studying these complicated systems. We highlight open questions in the field and suggest future directions. This minireview is part of a special collection of articles in memory of Professor Deborah Zamble, a leader in the field of nickel biochemistry.
Collapse
Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
7
|
Yang J, Peng Z, Zhu Q, Zhang J, Du G. [NiFe] Hydrogenase Accessory Proteins HypB-HypC Accelerate Proton Conversion to Enhance the Acid Resistance and d-Lactic Acid Production of Escherichia coli. ACS Synth Biol 2022; 11:1521-1530. [PMID: 35271275 DOI: 10.1021/acssynbio.1c00599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli is a major industrial producer of d-lactic acid due to its well-known advantages, such as short cycle times and low demand. However, acid sensitivity limits production capacity and increases costs. Enhancing the resistance of E. coli to acid stress is essential for improving the cell performance and production value. Here, we propose a feasible strategy to increase the acid tolerance of cells by strengthening intracellular proton conversion. The transcriptome test of the acid-tolerant adaptive evolution strain identified the hydrogenase accessory proteins HypB and HypC as a class of acid-tolerant factors that can assist the hydrogenase in catalyzing the reduction of protons to produce hydrogen. Strengthening the expression of HypB and HypC can increase the cell survival rate by 336.3 times during the lethal stress of d-lactate. In addition, HypB and HypC will assist d-lactate-producing strains to show higher sustainable productivity in an acidic fermentation environment, and d-lactate titer will increase by 113.6%. In order to further improve the expression system of the hydrogenase accessory protein, the introduction of a strong acid stress-driven promoter tdcAp can reduce the demand for neutralizer delivery in the fermentation process by about 26.7% while maintaining the maximum intensity of d-lactic acid production. Therefore, this research developed a method to improve the acid resistance of E. coli cells and reduce the cost of organic acid production by transforming protons.
Collapse
Affiliation(s)
- Jinhua Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Qi Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Hecel A, Kola A, Valensin D, Kozlowski H, Rowinska-Zyrek M. Metal specificity of the Ni(II) and Zn(II) binding sites of the N-terminal and G-domain of E. coli HypB. Dalton Trans 2021; 50:12635-12647. [PMID: 34545874 DOI: 10.1039/d1dt02126e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HypB is one of the chaperones required for proper nickel insertion into [NiFe]-hydrogenase. Escherichia coli HypB has two potential Ni(II) and Zn(II) binding sites-the N-terminal one and the so-called GTPase one. The metal-loaded HypB-SlyD metallochaperone complex activates nickel release from the N-terminal HypB site. In this work, we focus on the metal selectivity of the two HypB metal binding sites and show that (i) the N-terminal region binds Zn(II) and Ni(II) ions with higher affinity than the G-domain and (ii) the lower affinity G domain binds Zn(II) more effectively than Ni(II). In addition, the high affinity N-terminal domain, both in water and membrane mimicking SDS solution, has a larger affinity towards Zn(II) than Ni(II), while an opposite situation is observed at basic pH; at pH 7.4, the affinity of this region towards both metals is almost the same. The N-terminal HypB region is also more effective in Ni(II) binding than the previously studied SlyD metal binding regions. Considering that the nickel chaperone SlyD activates the release of nickel and blocks the release of zinc from the N-terminal high-affinity metal site of HypB, we may speculate that such pH-dependent metal affinity might modulate HypB interactions with SlyD, being dependent on both pH and the protein's metal status.
Collapse
Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
| | - Arian Kola
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Henryk Kozlowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland. .,Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland
| | | |
Collapse
|
10
|
Edmonds KA, Jordan MR, Giedroc DP. COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man. Metallomics 2021; 13:6327566. [PMID: 34302342 PMCID: PMC8360895 DOI: 10.1093/mtomcs/mfab046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023]
Abstract
Transition metal homeostasis ensures that cells and organisms obtain sufficient metal to meet cellular demand while dispensing with any excess so as to avoid toxicity. In bacteria, zinc restriction induces the expression of one or more Zur (zinc-uptake repressor)-regulated Cluster of Orthologous Groups (COG) COG0523 proteins. COG0523 proteins encompass a poorly understood sub-family of G3E P-loop small GTPases, others of which are known to function as metallochaperones in the maturation of cobalamin (CoII) and NiII cofactor-containing metalloenzymes. Here, we use genomic enzymology tools to functionally analyse over 80 000 sequences that are evolutionarily related to Acinetobacter baumannii ZigA (Zur-inducible GTPase), a COG0523 protein and candidate zinc metallochaperone. These sequences segregate into distinct sequence similarity network (SSN) clusters, exemplified by the ZnII-Zur-regulated and FeIII-nitrile hydratase activator CxCC (C, Cys; X, any amino acid)-containing COG0523 proteins (SSN cluster 1), NiII-UreG (clusters 2, 8), CoII-CobW (cluster 4), and NiII-HypB (cluster 5). A total of five large clusters that comprise ≈ 25% of all sequences, including cluster 3 which harbors the only structurally characterized COG0523 protein, Escherichia coli YjiA, and many uncharacterized eukaryotic COG0523 proteins. We also establish that mycobacterial-specific protein Y (Mpy) recruitment factor (Mrf), which promotes ribosome hibernation in actinomycetes under conditions of ZnII starvation, segregates into a fifth SSN cluster (cluster 17). Mrf is a COG0523 paralog that lacks all GTP-binding determinants as well as the ZnII-coordinating Cys found in CxCC-containing COG0523 proteins. On the basis of this analysis, we discuss new perspectives on the COG0523 proteins as cellular reporters of widespread nutrient stress induced by ZnII limitation.
Collapse
Affiliation(s)
- Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
11
|
Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
Collapse
Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Structural Insight into [NiFe] Hydrogenase Maturation by Transient Complexes between Hyp Proteins. Acc Chem Res 2020; 53:875-886. [PMID: 32227866 DOI: 10.1021/acs.accounts.0c00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
[NiFe] hydrogenases catalyze reversible hydrogen production/consumption. The core unit of [NiFe] hydrogenase consists of a large and a small subunit. The active site of the large subunit of [NiFe] hydrogenases contains a NiFe(CN)2CO cluster. The biosynthesis/maturation of these hydrogenases is a complex and dynamic process catalyzed primarily by six Hyp proteins (HypABCDEF), which play central roles in the maturation process. HypA and HypB are involved in the Ni insertion, whereas HypC, D, E, and F are required for the biosynthesis, assembly, and insertion of the Fe(CN)2CO group. HypE and HypF catalyze the synthesis of the CN group through the carbamoylation and cyanation of the C-terminus cysteine of HypE. HypC and HypD form a scaffold for the assembly of the Fe(CN)2CO moiety.Over the last decades, a large number of biochemical studies on maturation proteins have been performed, revealing basic functions of each Hyp protein and the overall framework of the maturation pathway. However, it is only in the last 10 years that structural insight has been gained, and our group has made significant contributions to the structural biology of hydrogenase maturation proteins.Since our first publication, where crystal structures of three Hyp proteins have been determined, we have performed a series of structural studies of all six Hyp proteins from a hyperthermophilic archaeon Thermococcus kodakarensis, providing molecular details of each Hyp protein. We have also determined the crystal structures of transient complexes between Hyp proteins that are formed during the maturation process to sequentially incorporate the components of the NiFe(CN)2CO cluster to immature large subunits of [NiFe] hydrogenases. Such complexes, whose crystal structures are determined, include HypA-HypB, HypA-HyhL (hydrogenase large subunit), HypC-HypD, and HypC-HypD-HypE. The structures of the HypC-HypD, and HypCDE complexes reveal a sophisticated process of transient formation of the HypCDE complex, providing insight into the molecular basis of Fe atom cyanation. The high-resolution structures of the carbamoylated and cyanated forms of HypE reveal a structural basis for the biological conversion of primary amide to nitrile. The structure of the HypA-HypB complex elucidates nucleotide-dependent transient complex formation between these two proteins and the molecular basis of acquisition and release of labile Ni. Furthermore, our recent structure analysis of a complex between HypA and immature HyhL reveals that spatial rearrangement of both the N- and C-terminal tails of HyhL will occur upon the [NiFe] cluster insertion, which function as a key checkpoint for the maturation completion. This Account will focus on recent advances in structural studies of the Hyp proteins and on mechanistic insights into the [NiFe] hydrogenase maturation.
Collapse
|
14
|
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.
Collapse
|
15
|
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.
Collapse
|
16
|
Lacasse MJ, Summers KL, Khorasani-Motlagh M, George GN, Zamble DB. Bimodal Nickel-Binding Site on Escherichia coli [NiFe]-Hydrogenase Metallochaperone HypA. Inorg Chem 2019; 58:13604-13618. [PMID: 31273981 DOI: 10.1021/acs.inorgchem.9b00897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[NiFe]-hydrogenase enzymes catalyze the reversible oxidation of hydrogen at a bimetallic cluster and are used by bacteria and archaea for anaerobic growth and pathogenesis. Maturation of the [NiFe]-hydrogenase requires several accessory proteins to assemble and insert the components of the active site. The penultimate maturation step is the delivery of nickel to a primed hydrogenase enzyme precursor protein, a process that is accomplished by two nickel metallochaperones, the accessory protein HypA and the GTPase HypB. Recent work demonstrated that nickel is rapidly transferred to HypA from GDP-loaded HypB within the context of a protein complex in a nickel selective and unidirectional process. To investigate the mechanism of metal transfer, we examined the allosteric effects of nucleotide cofactors and partner proteins on the nickel environments of HypA and HypB by using a combination of biochemical, microbiological, computational, and spectroscopic techniques. We observed that loading HypB with either GDP or a nonhydrolyzable GTP analogue resulted in a similar nickel environment. In addition, interaction with a mutant version of HypA with disrupted nickel binding, H2Q-HypA, does not induce substantial changes to the HypB G-domain nickel site. Instead, the results demonstrate that HypB modifies the acceptor site of HypA. Analysis of a peptide maquette derived from the N-terminus of HypA revealed that nickel is predominately coordinated by atoms from the N-terminal Met-His motif. Furthermore, HypA is capable of two nickel-binding modes at the N-terminus, a HypB-induced mode and a binding mode that mirrors the peptide maquette. Collectively, these results reveal that HypB brings about changes in the nickel coordination of HypA, providing a mechanism for the HypB-dependent control of the acquisition and release of nickel by HypA.
Collapse
Affiliation(s)
- Michael J Lacasse
- Department of Chemistry , University of Toronto , Toronto , Ontario M5S 3H6 , Canada
| | - Kelly L Summers
- Department of Chemistry , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C9 , Canada
| | | | - Graham N George
- Department of Geological Sciences , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5E2 , Canada
| | - Deborah B Zamble
- Department of Chemistry , University of Toronto , Toronto , Ontario M5S 3H6 , Canada.,Department of Biochemistry , University of Toronto , Toronto , Ontario M5S 1A8 , Canada
| |
Collapse
|
17
|
Allen KN, Entova S, Ray LC, Imperiali B. Monotopic Membrane Proteins Join the Fold. Trends Biochem Sci 2019; 44:7-20. [PMID: 30337134 PMCID: PMC6309722 DOI: 10.1016/j.tibs.2018.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.
Collapse
Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sonya Entova
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
18
|
Khorasani-Motlagh M, Lacasse MJ, Zamble DB. High-affinity metal binding by the Escherichia coli [NiFe]-hydrogenase accessory protein HypB is selectively modulated by SlyD. Metallomics 2018; 9:482-493. [PMID: 28352890 DOI: 10.1039/c7mt00037e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
[NiFe]-hydrogenase, which catalyzes the reversible conversion between hydrogen gas and protons, is a vital component of the metabolism of many pathogens. Maturation of [NiFe]-hydrogenase requires selective nickel insertion that is completed, in part, by the metallochaperones SlyD and HypB. Escherichia coli HypB binds nickel with sub-picomolar affinity, and the formation of the HypB-SlyD complex activates nickel release from the high-affinity site (HAS) of HypB. In this study, the metal selectivity of this process was investigated. Biochemical experiments revealed that the HAS of full length HypB can bind stoichiometric zinc. Moreover, in contrast to the acceleration of metal release observed with nickel-loaded HypB, SlyD blocks the release of zinc from the HypB HAS. X-ray absorption spectroscopy (XAS) demonstrated that SlyD does not impact the primary coordination sphere of nickel or zinc bound to the HAS of HypB. Instead, computational modeling and XAS of HypB loaded with nickel or zinc indicated that zinc binds to HypB with a different coordination sphere than nickel. The data suggested that Glu9, which is not a nickel ligand, directly coordinates zinc. These results were confirmed through the characterization of E9A-HypB, which afforded weakened zinc affinity compared to wild-type HypB but similar nickel affinity. This mutant HypB fully supports the production of [NiFe]-hydrogenase in E. coli. Altogether, these results are consistent with the model that the HAS of HypB functions as a nickel site during [NiFe]-hydrogenase enzyme maturation and that the metal selectivity is controlled by activation of metal release by SlyD.
Collapse
|
19
|
Grossman JD, Camire EJ, Perlstein DL. Approaches to Interrogate the Role of Nucleotide Hydrolysis by Metal Trafficking NTPases: The Nbp35-Cfd1 Iron-Sulfur Cluster Scaffold as a Case Study. Methods Enzymol 2018; 599:293-325. [PMID: 29746244 DOI: 10.1016/bs.mie.2017.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nucleotide hydrolases play integral yet poorly understood roles in several metallocluster biosynthetic pathways. For example, the cytosolic iron-sulfur cluster assembly (CIA) is initiated by the CIA scaffold, an ATPase which builds new iron-sulfur clusters for proteins localized to the cytosol and the nucleus in eukaryotic organisms. While in vivo studies have demonstrated the scaffold's nucleotide hydrolase domain is vital for its function, in vitro approaches have not revealed tight allosteric coupling between the cluster scaffolding site and the ATPase site. Thus, the role of ATP hydrolysis has been hard to pinpoint. Herein, we describe methods to probe the nucleotide affinity and hydrolysis activity of the CIA scaffold from yeast, which is comprised of two homologous polypeptides called Nbp35 and Cfd1. In particular, we report two different equilibrium binding assays that make use of commercially available fluorescent nucleotide analogs. Importantly, these assays can be applied to probe nucleotide affinity of both the apo- and holo-forms of the CIA scaffold. Generally, these fluorescent nucleotide analogs have been underutilized to probe metal trafficking NTPase because one of the most commonly used probes, mantATP, which is labeled with the methylanthraniloyl probe via the 2' or 3' sugar hydroxyls, has an absorption which overlaps with the UV-Vis features of many metal-binding proteins. However, by exploiting analogs like BODIPY-FL and trinitrophenyl-labeled nucleotides which have better photophysical properties for metalloprotein applications, these approaches have the potential to reveal the mechanistic underpinnings of NTPases required for metallocluster biosynthesis.
Collapse
|
20
|
Abstract
Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.
Collapse
|
21
|
Campanello GC, Lofgren M, Yokom AL, Southworth DR, Banerjee R. Switch I-dependent allosteric signaling in a G-protein chaperone-B 12 enzyme complex. J Biol Chem 2017; 292:17617-17625. [PMID: 28882898 DOI: 10.1074/jbc.m117.786095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/14/2017] [Indexed: 11/06/2022] Open
Abstract
G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for uncovering strategies deployed for allosteric signal transduction. MeaB is a multifunctional G-protein chaperone, which gates loading of the active 5'-deoxyadenosylcobalamin cofactor onto methylmalonyl-CoA mutase (MCM) and precludes loading of inactive cofactor forms. MeaB also safeguards MCM, which uses radical chemistry, against inactivation and rescues MCM inactivated during catalytic turnover by using the GTP-binding energy to offload inactive cofactor. The conserved switch I and II signaling motifs used by G-proteins are predicted to mediate allosteric regulation in response to nucleotide binding and hydrolysis in MeaB. Herein, we targeted conserved residues in the MeaB switch I motif to interrogate the function of this loop. Unexpectedly, the switch I mutations had only modest effects on GTP binding and on GTPase activity and did not perturb stability of the MCM-MeaB complex. However, these mutations disrupted multiple MeaB chaperone functions, including cofactor editing, loading, and offloading. Hence, although residues in the switch I motif are not essential for catalysis, they are important for allosteric regulation. Furthermore, single-particle EM analysis revealed, for the first time, the overall architecture of the MCM-MeaB complex, which exhibits a 2:1 stoichiometry. These EM studies also demonstrate that the complex exhibits considerable conformational flexibility. In conclusion, the switch I element does not significantly stabilize the MCM-MeaB complex or influence the affinity of MeaB for GTP but is required for transducing signals between MeaB and MCM.
Collapse
Affiliation(s)
- Gregory C Campanello
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
| | - Michael Lofgren
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
| | - Adam L Yokom
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and.,the Department of Biological Chemistry and.,the Graduate Program in Chemical Biology, Life Sciences Institute, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Daniel R Southworth
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and.,the Department of Biological Chemistry and
| | - Ruma Banerjee
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
| |
Collapse
|
22
|
Palombo M, Bonucci A, Etienne E, Ciurli S, Uversky VN, Guigliarelli B, Belle V, Mileo E, Zambelli B. The relationship between folding and activity in UreG, an intrinsically disordered enzyme. Sci Rep 2017; 7:5977. [PMID: 28729736 PMCID: PMC5519622 DOI: 10.1038/s41598-017-06330-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/12/2017] [Indexed: 12/02/2022] Open
Abstract
A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease. The effect of denaturants and osmolytes on protein structure and activity was analyzed using circular dichroism (CD), Site-Directed Spin Labeling (SDSL) coupled to EPR spectroscopy, and enzymatic assays. Our data show that SpUreG needs a "flexibility window" to be catalytically competent, with both too low and too high mobility being detrimental for its activity.
Collapse
Affiliation(s)
- Marta Palombo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy
| | - Alessio Bonucci
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Emilien Etienne
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, MDC07, USA
| | - Bruno Guigliarelli
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Valérie Belle
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France
| | - Elisabetta Mileo
- Aix-Marseille Univ, CNRS, IMM (FR 3479), BIP (UMR 7281), 31 chemin Joseph Aiguier, Marseille, 13402, France.
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna, 40127, Italy.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Zeer-Wanklyn CJ, Zamble DB. Microbial nickel: cellular uptake and delivery to enzyme centers. Curr Opin Chem Biol 2017; 37:80-88. [PMID: 28213182 DOI: 10.1016/j.cbpa.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 01/29/2023]
Abstract
Nickel enzymes allow microorganisms to access chemistry that can be vital for survival and virulence. In this review we highlight recent work on several systems that import nickel ions and deliver them to the active sites of these enzymes. Small molecules, in particular l-His and derivatives, may chelate nickel ions before import at TonB-dependent outer-membrane and ABC-type inner-membrane transporters. Inside the cell, nickel ions are used by maturation factors required to produce nickel enzymes such as [NiFe]-hydrogenase, urease and lactate racemase. These accessory proteins often exhibit metal selectivity and frequently include an NTP-hydrolyzing metallochaperone protein. The research described provides a deeper understanding of the processes that allow microorganisms to access nickel ions from the environment and incorporate them into nickel proteins.
Collapse
Affiliation(s)
- Conor J Zeer-Wanklyn
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
| |
Collapse
|
25
|
Lacasse MJ, Douglas CD, Zamble DB. Mechanism of Selective Nickel Transfer from HypB to HypA, Escherichia coli [NiFe]-Hydrogenase Accessory Proteins. Biochemistry 2016; 55:6821-6831. [PMID: 27951644 DOI: 10.1021/acs.biochem.6b00706] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[NiFe]-hydrogenase enzymes catalyze the reversible reduction of protons to molecular hydrogen and serve as a vital component of the metabolism of many pathogens. The synthesis of the bimetallic catalytic center requires a suite of accessory proteins, and the penultimate step, nickel insertion, is facilitated by the metallochaperones HypA and HypB. In Escherichia coli, nickel moves from a site in the GTPase domain of HypB to HypA in a process accelerated by GDP. To determine how the transfer of nickel is controlled, the impacts of HypA and nucleotides on the properties of HypB were examined. Integral to this work was His2Gln HypA, a mutant with attenuated nickel affinity that does not support hydrogenase production in E. coli. This mutation inhibits the translocation of nickel from HypB. H2Q-HypA does not modulate the apparent metal affinity of HypB, but the stoichiometry and stability of the HypB-nickel complex are modulated by the nucleotide. Furthermore, the HypA-HypB interaction was detected by gel filtration chromatography if HypB was loaded with GDP, but not a GTP analogue, and the protein complex dissociated upon binding of nickel to His2 of HypA. In contrast, a nucleotide does not modulate the binding of zinc to HypB, and loading zinc into the GTPase domain of HypB inhibits formation of the complex with HypA. These results demonstrate that GTP hydrolysis controls both metal binding and protein-protein interactions, conferring selective and directional nickel transfer during [NiFe]-hydrogenase biosynthesis.
Collapse
Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Colin D Douglas
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
26
|
Mazzantini D, Celandroni F, Salvetti S, Gueye SA, Lupetti A, Senesi S, Ghelardi E. FlhF Is Required for Swarming Motility and Full Pathogenicity of Bacillus cereus. Front Microbiol 2016; 7:1644. [PMID: 27807433 PMCID: PMC5069341 DOI: 10.3389/fmicb.2016.01644] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/03/2016] [Indexed: 11/13/2022] Open
Abstract
Besides sporulation, Bacillus cereus can undergo a differentiation process in which short swimmer cells become elongated and hyperflagellated swarmer cells that favor migration of the bacterial community on a surface. The functionally enigmatic flagellar protein FlhF, which is the third paralog of the signal recognition particle (SRP) GTPases Ffh and FtsY, is required for swarming in many bacteria. Previous data showed that FlhF is involved in the control of the number and positioning of flagella in B. cereus. In this study, in silico analysis of B. cereus FlhF revealed that this protein presents conserved domains that are typical of SRPs in many organisms and a peculiar N-terminal basic domain. By proteomic analysis, a significant effect of FlhF depletion on the amount of secreted proteins was found with some proteins increased (e.g., B component of the non-hemolytic enterotoxin, cereolysin O, enolase) and others reduced (e.g., flagellin, L2 component of hemolysin BL, bacillolysin, sphingomyelinase, PC-PLC, PI-PLC, cytotoxin K) in the extracellular proteome of a ΔflhF mutant. Deprivation of FlhF also resulted in significant attenuation in the pathogenicity of this strain in an experimental model of infection in Galleria mellonella larvae. Our work highlights the multifunctional role of FlhF in B. cereus, being this protein involved in bacterial flagellation, swarming, protein secretion, and pathogenicity.
Collapse
Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sara Salvetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sokhna A Gueye
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sonia Senesi
- Department of Biology, University of Pisa Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of PisaPisa, Italy; Research Center Nutraceuticals and Food for Health-Nutrafood, University of PisaPisa, Italy
| |
Collapse
|
27
|
Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
Collapse
Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
28
|
Denny JA, Foley WS, Todd AD, Darensbourg MY. The ligand unwrapping/rewrapping pathway that exchanges metals in S-acetylated, hexacoordinate N 2S 2O 2 complexes. Chem Sci 2015; 6:7079-7088. [PMID: 29896341 PMCID: PMC5954489 DOI: 10.1039/c5sc02269j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/05/2015] [Indexed: 12/13/2022] Open
Abstract
The effect of S-acetylation in MN2S2 complexes on metal exchange reactivity was examined in a series of MN2S2O2 complexes.
The effect of S-acetylation in MN2S2 complexes on metal exchange reactivity was examined in a series of MN2S2O2 complexes. While clean exchange processes do not occur for the MN2S2 derivatives where formation of S-bridged aggregates predominate, acetylation permits the metal exchange with hierarchy that follows the Irving–Williams series of stability for first row transition metals: Fe2+ < Co2+ < Ni2+ < Cu2+ > Zn2+. The rate determining step consistent with kinetic parameters depends on both M and M′, supporting a mechanism of exchange that involves ligand unwrapping/rewrapping process as earlier defined by Margerum et al. for M(EDTA) systems. The enhanced metal exchange deriving from S-acetylation is of significance to probes and detection of cysteine-S metallo-proteins and metallo-enzyme active sites, and highlights a new role for S-acetylation.
Collapse
Affiliation(s)
- J A Denny
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - W S Foley
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - A D Todd
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| | - M Y Darensbourg
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , USA .
| |
Collapse
|
29
|
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.
Collapse
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.
| |
Collapse
|
30
|
Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer. Proc Natl Acad Sci U S A 2015; 112:7701-6. [PMID: 26056269 DOI: 10.1073/pnas.1503102112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Ni atom at the catalytic center of [NiFe] hydrogenases is incorporated by a Ni-metallochaperone, HypA, and a GTPase/ATPase, HypB. We report the crystal structures of the transient complex formed between HypA and ATPase-type HypB (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT can interact with HypA and induces drastic conformational changes of HypA. Consequently, upon complex formation, a conserved His residue of HypA comes close to the N-terminal conserved motif of HypA and forms a Ni-binding site, to which a Ni ion is bound with a nearly square-planar geometry. The Ni binding site in the HypABAT complex has a nanomolar affinity (Kd = 7 nM), which is in contrast to the micromolar affinity (Kd = 4 µM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypBAT, affecting its association with HypA. These findings indicate that HypA and HypBAT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypBAT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA.
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Manfredi Miraula
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
| | | | | |
Collapse
|
32
|
Visualization of a radical B12 enzyme with its G-protein chaperone. Proc Natl Acad Sci U S A 2015; 112:2419-24. [PMID: 25675500 DOI: 10.1073/pnas.1419582112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G-protein metallochaperones ensure fidelity during cofactor assembly for a variety of metalloproteins, including adenosylcobalamin (AdoCbl)-dependent methylmalonyl-CoA mutase and hydrogenase, and thus have both medical and biofuel development applications. Here, we present crystal structures of IcmF, a natural fusion protein of AdoCbl-dependent isobutyryl-CoA mutase and its corresponding G-protein chaperone, which reveal the molecular architecture of a G-protein metallochaperone in complex with its target protein. These structures show that conserved G-protein elements become ordered upon target protein association, creating the molecular pathways that both sense and report on the cofactor loading state. Structures determined of both apo- and holo-forms of IcmF depict both open and closed enzyme states, in which the cofactor-binding domain is alternatively positioned for cofactor loading and for catalysis. Notably, the G protein moves as a unit with the cofactor-binding domain, providing a visualization of how a chaperone assists in the sequestering of a precious cofactor inside an enzyme active site.
Collapse
|
33
|
Peters JW, Schut GJ, Boyd ES, Mulder DW, Shepard EM, Broderick JB, King PW, Adams MWW. [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1350-69. [PMID: 25461840 DOI: 10.1016/j.bbamcr.2014.11.021] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/10/2014] [Accepted: 11/16/2014] [Indexed: 11/29/2022]
Abstract
The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
34
|
Xia W, Li H, Sun H. Functional disruption of HypB, a GTPase of Helicobacter pylori, by bismuth. Chem Commun (Camb) 2014; 50:1611-4. [PMID: 24389922 DOI: 10.1039/c3cc47644h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bismuth (Bi(3+)) binds equal molar amounts of HypB from Helicobacter pylori at the conserved metal site with a dissociation constant of 0.94 (±0.25) × 10(-17) μM, and concomitantly induces the protein dimerization similarly to Ni(2+). Excess Bi(3+) causes HypB further oligomerization, leading to HypB GTPase dysfunction. The results extend our understanding on the inhibitory mechanism of bismuth drugs against the pathogen.
Collapse
Affiliation(s)
- Wei Xia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China.
| | | | | |
Collapse
|
35
|
Expression of Rat Sperm Flagellum-Movement Associated Protein Genes under 2,3,7,8-Tetrachlorodibenzo-p-dioxin Treatment. Biosci Biotechnol Biochem 2014; 73:946-9. [DOI: 10.1271/bbb.80764] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
37
|
Sydor AM, Lebrette H, Ariyakumaran R, Cavazza C, Zamble DB. Relationship between Ni(II) and Zn(II) coordination and nucleotide binding by the Helicobacter pylori [NiFe]-hydrogenase and urease maturation factor HypB. J Biol Chem 2014; 289:3828-41. [PMID: 24338018 PMCID: PMC3924253 DOI: 10.1074/jbc.m113.502781] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/01/2013] [Indexed: 12/23/2022] Open
Abstract
The pathogen Helicobacter pylori requires two nickel-containing enzymes, urease and [NiFe]-hydrogenase, for efficient colonization of the human gastric mucosa. These enzymes possess complex metallocenters that are assembled by teams of proteins in multistep pathways. One essential accessory protein is the GTPase HypB, which is required for Ni(II) delivery to [NiFe]-hydrogenase and participates in urease maturation. Ni(II) or Zn(II) binding to a site embedded in the GTPase domain of HypB modulates the enzymatic activity, suggesting a mechanism of regulation. In this study, biochemical and structural analyses of H. pylori HypB (HpHypB) revealed an intricate link between nucleotide and metal binding. HpHypB nickel coordination, stoichiometry, and affinity were modulated by GTP and GDP, an effect not observed for zinc, and biochemical evidence suggests that His-107 coordination to nickel toggles on and off in a nucleotide-dependent manner. These results are consistent with the crystal structure of HpHypB loaded with Ni(II), GDP, and Pi, which reveals a nickel site distinct from that of zinc-loaded Methanocaldococcus jannaschii HypB as well as subtle changes to the protein structure. Furthermore, Cys-142, a metal ligand from the Switch II GTPase motif, was identified as a key component of the signal transduction between metal binding and the enzymatic activity. Finally, potassium accelerated the enzymatic activity of HpHypB but had no effect on the other biochemical properties of the protein. Altogether, this molecular level information about HpHypB provides insight into its cellular function and illuminates a possible mechanism of metal ion discrimination.
Collapse
Affiliation(s)
- Andrew M. Sydor
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
| | - Hugo Lebrette
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), CEA, DSV, IBS and CNRS, IBS, F-38000 Grenoble, France
| | - Rishikesh Ariyakumaran
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
| | - Christine Cavazza
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), CEA, DSV, IBS and CNRS, IBS, F-38000 Grenoble, France
| | - Deborah B. Zamble
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
| |
Collapse
|
38
|
Cheng T, Li H, Yang X, Xia W, Sun H. Interaction of SlyD with HypB of Helicobacter pylori facilitates nickel trafficking. Metallomics 2014; 5:804-7. [PMID: 23708681 DOI: 10.1039/c3mt00014a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SlyD from Helicobacter pylori interacts with the [NiFe] hydrogenase accessory protein HypB through its IF domain. HpSlyD delivers Ni(2+) to HpHypB, leading to the enhancement of GTPase activity of HpHypB and implying the facilitation of Ni(2+) delivery from HpHypB to [NiFe] hydrogenase.
Collapse
Affiliation(s)
- Tianfan Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | | | | | | | | |
Collapse
|
39
|
Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc Natl Acad Sci U S A 2013; 110:20485-90. [PMID: 24297906 PMCID: PMC3870729 DOI: 10.1073/pnas.1313620110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hydrogenase pleiotropically acting protein (Hyp)E plays a role in biosynthesis of the cyano groups for the NiFe(CN)2CO center of [NiFe] hydrogenases by catalyzing the ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, until now there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. Here, we report the crystal structures of the carbamoylated and cyanated forms of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53- and 1.64-Å resolution, respectively. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. In the presence of ATP, the thiocarboxamide of Cys338 is successfully dehydrated into the thiocyanate. In the carbamoylated state, the thiocarboxamide nitrogen atom of Cys338 is close to a conserved glutamate residue (Glu272), but the spatial position of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. The close contact of Lys134 with an arginine residue lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively.
Collapse
Affiliation(s)
- Taiga Tominaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Watanabe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Rie Matsumi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan; and
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
40
|
Lisher JP, Higgins KA, Maroney MJ, Giedroc DP. Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry 2013; 52:7689-701. [PMID: 24067066 DOI: 10.1021/bi401132w] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Transition metals, including manganese, are required for the proper virulence and persistence of many pathogenic bacteria. In Streptococcus pneumoniae (Spn), manganese homeostasis is controlled by a high-affinity Mn(II) uptake complex, PsaBCA, and a constitutively expressed efflux transporter, MntE. psaBCA expression is transcriptionally regulated by the DtxR/MntR family metalloregulatory protein pneumococcal surface antigen repressor (PsaR) in Spn. Here, we present a comprehensive analysis of the metal and DNA binding properties of PsaR. PsaR is a homodimer in the absence and presence of metals and binds two manganese or zinc atoms per protomer (four per dimer) in two pairs of structurally distinct sites, termed site 1 and site 2. Site 1 is likely filled with Zn(II) in vivo (K(Zn1) ≥ 10¹³ M⁻¹; K(Mn1) ≈ 10⁸ M⁻¹). The Zn(II)-site 1 complex adopts a pentacoordinate geometry as determined by X-ray absorption spectroscopy containing a single cysteine and appears to be analogous to the Cd(II) site observed in Streptococcus gordonii ScaR. Site 1 is necessary but not sufficient for full positive allosteric activation of DNA operator binding by metals as measured by ΔGc, the allosteric coupling free energy, because site 1 mutants show an intermediate ΔGc. Site 2 is the primary regulatory site and governs specificity for Mn(II) over Zn(II) in PsaR, where ΔGc(Zn,Mn) >> ΔGc(Zn,Zn) despite the fact that Zn(II) binds site 2 with an affinity 40-fold higher than that of Mn(II); i.e., K(Zn2) > K(Mn2). Mutational studies reveal that Asp7 in site 2 is a critical ligand for Mn(II)-dependent allosteric activation of DNA binding. These findings are discussed in the context of other well-studied DtxR/MntR Mn(II)/Fe(II) metallorepressors.
Collapse
Affiliation(s)
- John P Lisher
- Department of Chemistry and ‡Interdisciplinary Graduate Program in Biochemistry, Indiana University , Bloomington, Indiana 47405-7102, United States
| | | | | | | |
Collapse
|
41
|
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.
Collapse
|
42
|
Farrugia MA, Han L, Zhong Y, Boer JL, Ruotolo BT, Hausinger RP. Analysis of a soluble (UreD:UreF:UreG)2 accessory protein complex and its interactions with Klebsiella aerogenes urease by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1328-1337. [PMID: 23797863 PMCID: PMC3788043 DOI: 10.1007/s13361-013-0677-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/10/2013] [Accepted: 05/10/2013] [Indexed: 06/02/2023]
Abstract
Maturation of the nickel-containing urease of Klebsiella aerogenes is facilitated by the UreD, UreF, and UreG accessory proteins along with the UreE metallo-chaperone. A fusion of the maltose binding protein and UreD (MBP-UreD) was co-isolated with UreF and UreG in a soluble complex possessing a (MBPUreD: UreF:UreG)2 quaternary structure. Within this complex a UreF:UreF interaction was identified by chemical cross-linking of the amino termini of its two UreF protomers, as shown by mass spectrometry of tryptic peptides. A preactivation complex was formed by the interaction of (MBP-UreD:UreF:UreG)2 and urease. Mass spectrometry of intact protein species revealed a pathway for synthesis of the urease pre-activation complex in which individual hetero-trimer units of the (MBP-UreD:UreF:UreG)2 complex bind to urease. Together, these data provide important new insights into the structures of protein complexes associated with urease activation.
Collapse
Affiliation(s)
- Mark A. Farrugia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Linjie Han
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Yueyang Zhong
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Jodi L. Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
43
|
Lofgren M, Koutmos M, Banerjee R. Autoinhibition and signaling by the switch II motif in the G-protein chaperone of a radical B12 enzyme. J Biol Chem 2013; 288:30980-9. [PMID: 23996001 DOI: 10.1074/jbc.m113.499970] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MeaB is an accessory GTPase protein involved in the assembly, protection, and reactivation of 5'-deoxyadenosyl cobalamin-dependent methylmalonyl-CoA mutase (MCM). Mutations in the human ortholog of MeaB result in methylmalonic aciduria, an inborn error of metabolism. G-proteins typically utilize conserved switch I and II motifs for signaling to effector proteins via conformational changes elicited by nucleotide binding and hydrolysis. Our recent discovery that MeaB utilizes an unusual switch III region for bidirectional signaling with MCM raised questions about the roles of the switch I and II motifs in MeaB. In this study, we addressed the functions of conserved switch II residues by performing alanine-scanning mutagenesis. Our results demonstrate that the GTPase activity of MeaB is autoinhibited by switch II and that this loop is important for coupling nucleotide-sensitive conformational changes in switch III to elicit the multiple chaperone functions of MeaB. Furthermore, we report the structure of MeaB·GDP crystallized in the presence of AlFx(-) to form the putative transition state analog, GDP·AlF4(-). The resulting crystal structure and its comparison with related G-proteins support the conclusion that the catalytic site of MeaB is incomplete in the absence of the GTPase-activating protein MCM and therefore unable to stabilize the transition state analog. Favoring an inactive conformation in the absence of the client MCM protein might represent a strategy for suppressing the intrinsic GTPase activity of MeaB in which the switch II loop plays an important role.
Collapse
Affiliation(s)
- Michael Lofgren
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
| | | | | |
Collapse
|
44
|
A switch III motif relays signaling between a B12 enzyme and its G-protein chaperone. Nat Chem Biol 2013; 9:535-9. [PMID: 23873214 PMCID: PMC3752380 DOI: 10.1038/nchembio.1298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 06/24/2013] [Indexed: 01/17/2023]
Abstract
Fidelity during cofactor assembly is essential for the proper functioning of metalloenzymes and is ensured by specific chaperones. MeaB, a G-protein chaperone for the coenzyme B12-dependent radical enzyme, methylmalonyl-CoA mutase (MCM), utilizes the energy of GTP binding and/or hydrolysis to regulate cofactor loading into MCM, protect MCM from inactivation, and rescue MCM inactivated during turnover. Typically, G-proteins signal to client proteins using the conformationally mobile switch I and II loops. Crystallographic snapshots of MeaB reported herein reveal a novel switch III element, which exhibits substantial conformational plasticity. Using alanine-scanning mutagenesis, we demonstrate that the switch III motif is critical for bidirectional signal transmission of the GTPase activating protein activity of MCM and the chaperone functions of MeaB in the MeaB:MCM complex. Mutations in the switch III loop identified in patients corrupt this inter-protein communication and lead to methylmalonic aciduria, an inborn error of metabolism.
Collapse
|
45
|
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.
Collapse
|
46
|
Musiani F, Ippoliti E, Micheletti C, Carloni P, Ciurli S. Conformational fluctuations of UreG, an intrinsically disordered enzyme. Biochemistry 2013; 52:2949-54. [PMID: 23560717 DOI: 10.1021/bi4001744] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UreG proteins are small GTP binding (G) proteins that catalyze the hydrolysis of GTP necessary for the maturation of urease, a virulence factor in bacterial pathogenesis. UreG proteins are the first documented cases of intrinsically disordered enzymes. The comprehension of the dynamics of folding-unfolding events occurring in this protein could shed light on the enzymatic mechanism of UreG. Here, we used the recently developed replica exchange with solute tempering (REST2) computational methodology to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations. The same simulation and analysis protocol has been applied to HypB from Methanocaldococcus jannaschii (MjHypB), which is closely related to UreG in both sequence and function, even though it is not intrinsically disordered. A comparison of the two systems reveals that both HpUreG and MjHypB feature a substantial rigidity of the protein regions involved in catalysis, justifying its residual catalytic activity. On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallochaperones necessary for the formation of multiprotein complexes known to be involved in urease activation.
Collapse
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | | | | |
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- Mark A Farrugia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | | |
Collapse
|
48
|
Sydor A, Jost M, Ryan KS, Turo KE, Douglas C, Drennan CL, Zamble DB. Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases. Biochemistry 2013; 52:1788-1801. [PMID: 24449932 PMCID: PMC3596956 DOI: 10.1021/bi301600z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GTPases are critical molecular switches involved in a wide range of biological functions. Recent phylogenetic and genomic analyses of the large, mostly uncharacterized COG0523 subfamily of GTPases revealed a link between some COG0523 proteins and metal homeostasis pathways. In this report, we detail the bioinorganic characterization of YjiA, a representative member of COG0523 subgroup 9 and the only COG0523 protein to date with high-resolution structural information. We find that YjiA is capable of binding several types of transition metals with dissociation constants in the low micromolar range and that metal binding affects both the oligomeric structure and GTPase activity of the enzyme. Using a combination of X-ray crystallography and site-directed mutagenesis, we identify, among others, a metal-binding site adjacent to the nucleotide-binding site in the GTPase domain that involves a conserved cysteine and several glutamate residues. Mutations of the coordinating residues decrease the impact of metal, suggesting that metal binding to this site is responsible for modulating the GTPase activity of the protein. These findings point toward a regulatory function for these COG0523 GTPases that is responsive to their metal-bound state.
Collapse
Affiliation(s)
- Andrew
M. Sydor
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6
| | - Marco Jost
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Katherine S. Ryan
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Kaitlyn E. Turo
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Colin
D. Douglas
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6
| | - Catherine L. Drennan
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States,C.L.D.:
telephone, (617)
253-5622; fax, (617) 258-7847; e-mail, . D.B.Z.: telephone, (416) 978-3568; e-mail,
| | - Deborah B. Zamble
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6,C.L.D.:
telephone, (617)
253-5622; fax, (617) 258-7847; e-mail, . D.B.Z.: telephone, (416) 978-3568; e-mail,
| |
Collapse
|
49
|
Sasaki D, Watanabe S, Matsumi R, Shoji T, Yasukochi A, Tagashira K, Fukuda W, Kanai T, Atomi H, Imanaka T, Miki K. Identification and structure of a novel archaeal HypB for [NiFe] hydrogenase maturation. J Mol Biol 2013; 425:1627-40. [PMID: 23399544 DOI: 10.1016/j.jmb.2013.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/01/2013] [Accepted: 02/04/2013] [Indexed: 11/17/2022]
Abstract
HypB (metal-binding GTPase) and HypA (nickel metallochaperone) are required for nickel insertion into [NiFe] hydrogenase. However, the HypB homolog proteins are not found in some archaeal species including Thermococcales. In this article, we identify a novel archaeal Mrp/MinD family ATPase-type HypB from Thermococcus kodakarensis (Tk-mmHypB) and determine its crystal structure. The mmhypB gene is conserved among species lacking the hypB gene and is located adjacent to the hypA gene on their genome. Deletion of the mmhypB gene leads to a significant reduction in hydrogen-dependent growth of T. kodakarensis, which is restored by nickel supplementation. The monomer structure of Tk-mmHypB is similar to those of the Mrp/MinD family ATPases. The ADP molecules are tightly bound to the protein. Isothermal titration calorimetry shows that Tk-mmHypB binds ATP with a K(d) value of 84 nM. ADP binds more tightly than does ATP, with a K(d) value of 15 nM. The closed Tk-mmHypB dimer in the crystallographic asymmetric unit is consistent with the ATP-hydrolysis-deficient dimer of the Mrp/MinD family Soj/MinD proteins. Structural comparisons with these proteins suggest the ATP-binding dependent conformational change and rearrangement of the Tk-mmHypB dimer. These observations imply that the nickel insertion process during the [NiFe] hydrogenase maturation is performed by HypA, mmHypB, and a nucleotide exchange factor in these archaea.
Collapse
Affiliation(s)
- Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Higgins KA, Hu HQ, Chivers PT, Maroney MJ. Effects of select histidine to cysteine mutations on transcriptional regulation by Escherichia coli RcnR. Biochemistry 2012; 52:84-97. [PMID: 23215580 DOI: 10.1021/bi300886q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RcnR metalloregulator represses the transcription of the Co(II) and Ni(II) exporter, RcnAB. Previous studies have shown that Co(II) and Ni(II) bind to RcnR in six-coordinate sites, resulting in derepression. Here, the roles of His60, His64, and His67 in specific metal recognition are examined. His60 and His64 correspond to ligands that are important for Cu(I) binding in the homologous Cu(I)-responsive metalloregulator, CsoR. These residues are known to be functionally important in RcnR transcriptional regulation. X-ray absorption spectroscopy (XAS) was used to examine the structure of bound cognate and noncognate metal ions, and lacZ reporter assays were used to assess the transcription of rcnA in response to metal binding in the three His → Cys mutations, H60C, H64C, and H67C. These studies confirm that both Ni(II) and Co(II) use His64 as a ligand. H64C-RcnR is also the only known mutant that retains a Co(II) response while eliminating the response to Ni(II) binding. XAS data indicate that His60 and His67 are potential Co(II) ligands. The effects of the mutations of His60, His64, and His67 on the structures of the noncognate metal ions [Zn(II) and Cu(I)] reveal that these residues have distinctive roles in binding noncognate metals. None of the His → Cys mutants in RcnR confer any response to Cu(I) binding, including H64C-RcnR, where the ligands involved in Cu(I) binding in CsoR are present. These data indicate that while the secondary, tertiary, and quaternary structures of CsoR and RcnR are quite similar, small changes in primary sequence reveal that the specific mechanisms involved in metal recognition are quite different.
Collapse
Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | | |
Collapse
|