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Bárdy P, MacDonald CI, Pantůček R, Antson AA, Fogg PC. Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales. iScience 2023; 26:108104. [PMID: 37867962 PMCID: PMC10589892 DOI: 10.1016/j.isci.2023.108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/23/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Although membrane-containing dsDNA bacterial viruses are some of the most prevalent predators in aquatic environments, we know little about how they function due to their intractability in the laboratory. Here, we have identified and thoroughly characterized a new type of membrane-containing bacteriophage, Jorvik, that infects the freshwater mixotrophic model bacterium Rhodobacter capsulatus. Jorvik is extremely virulent, can persist in the host integrated into the RuBisCo operon and encodes two experimentally verified cell wall hydrolases. Jorvik-like prophages are abundant in the genomes of Alphaproteobacteria, are distantly related to known viruses of the class Tectiliviricetes, and we propose they should be classified as a new family. Crucially, we demonstrate how widely used phage manipulation methods should be adjusted to prevent loss of virus infectivity. Our thorough characterization of environmental phage Jorvik provides important experimental insights about phage diversity and interactions in microbial communities that are often unexplored in common metagenomic analyses.
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Affiliation(s)
- Pavol Bárdy
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Conor I.W. MacDonald
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
| | - Paul C.M. Fogg
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
- Biology Department, University of York, Wentworth Way, York YO10 5DD, UK
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2
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Hawkins DEDP, Bayfield O, Fung HKH, Grba DN, Huet A, Conway J, Antson AA. Insights into a viral motor: the structure of the HK97 packaging termination assembly. Nucleic Acids Res 2023; 51:7025-7035. [PMID: 37293963 PMCID: PMC10359639 DOI: 10.1093/nar/gkad480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alexis Huet
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James F Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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3
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Chechik M, Greive SJ, Antson AA, Jenkins HT. Structure of HK97 small terminase:DNA complex unveils a novel DNA binding mechanism by a circular protein. bioRxiv 2023:2023.07.17.549218. [PMID: 37503206 PMCID: PMC10370121 DOI: 10.1101/2023.07.17.549218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for three archetypal bacteriophage systems: cos, pac and phi29. We identified the minimal site within the cos region of bacteriophage HK97 specifically recognised by the small terminase and determined a cryoEM structure for the small terminase:DNA complex. This nonameric circular protein utilizes a previously unknown mechanism of DNA binding. While DNA threads through the central tunnel, unexpectedly, DNA-recognition is generated at its exit by a substructure formed by the N- and C-terminal segments of two adjacent protomers of the terminase which are unstructured in the absence of DNA. Such interaction ensures continuous engagement of the small terminase with DNA, allowing sliding along DNA while simultaneously checking the DNA sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the cos site.
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Affiliation(s)
- Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | | | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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4
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Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA. Structural atlas of a human gut crassvirus. Nature 2023; 617:409-416. [PMID: 37138077 PMCID: PMC10172136 DOI: 10.1038/s41586-023-06019-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals1-4. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
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Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ekaterina V Khokhlova
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
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5
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Tugaeva KV, Sysoev AA, Kapitonova AA, Smith JLR, Zhu P, Cooley RB, Antson AA, Sluchanko NN. Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J Mol Biol 2023; 435:167891. [PMID: 36427566 PMCID: PMC9683861 DOI: 10.1016/j.jmb.2022.167891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
Abstract
Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of SARS-CoV-2 nucleoprotein at either of two pseudo-repeats centered at Ser197 and Thr205. According to fluorescence anisotropy measurements, the pT205-motif,presentin SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which collectively display an unforeseen pT205/pS197 peptide binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data obtained on the full protein-protein complex indicate that 14-3-3 binding occludes the Ser/Arg-rich region of the nucleoprotein, inhibiting its dephosphorylation. This Ser/Arg-rich region is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting that the strength of 14-3-3/nucleoprotein interaction can be linked with the replicative fitness of the virus.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Phillip Zhu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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6
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Mojtabavi M, Greive SJ, Antson AA, Wanunu M. High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized within a Solid-State Nanopore. J Am Chem Soc 2022; 144:22540-22548. [PMID: 36455212 DOI: 10.1021/jacs.2c08514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The application of nanopores as label-free, single-molecule biosensors for electrical or optical probing of structural features in biomolecules has been widely explored. While biological nanopores (membrane proteins and bacteriophage portal proteins) and solid-state nanopores (thin films and two-dimensional materials) have been extensively employed, the third class of nanopores known as hybrid nanopores, where an artificial membrane substitutes the organic support membrane of proteins, has been only sparsely studied due to challenges in implementation. G20c portal protein contains a natural DNA pore that is used by viruses for filling their capsid with viral genomic DNA. We have previously developed a lipid-free hybrid nanopore by "corking" the G20c portal protein into a SiNx nanopore. Herein, we demonstrate that through chemical functionalization of the synthetic nanopore, covalent linkage between the solid-state pore and the G20c portal protein considerably improves the hybrid pore stability, lifetime, and voltage resilience. Moreover, we demonstrate electric-field-driven and motor protein-mediated transport of DNA molecules through this hybrid nanopore. Our integrated protein/solid-state device can serve as a robust and durable framework for sensing and sequencing at high voltages, potentially providing higher resolution, higher signal-to-noise ratio, and higher throughput compared to the more conventional membrane-embedded protein platforms.
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Affiliation(s)
- Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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7
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Ker DS, Jenkins HT, Greive SJ, Antson AA. CryoEM structure of the Nipah virus nucleocapsid assembly. PLoS Pathog 2021; 17:e1009740. [PMID: 34270629 PMCID: PMC8318291 DOI: 10.1371/journal.ppat.1009740] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/28/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the “3-bases-in, 3-bases-out” conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123–139, which may serve as a valuable epitope for surveillance and diagnostics. Nipah virus is a highly pathogenic RNA virus which, along with the closely related Hendra virus, emerged relatively recently. Due to ~40% mortality rate and evidence of animal-to-human as well as human-to-human transmission, development of antivirals against the Nipah and henipaviral disease is particularly urgent. In common with other single-stranded RNA viruses, including Ebola and coronaviruses, the nucleocapsid assembly of the Nipah virus safeguards the viral genome, protecting it from degradation and facilitating its encapsidation and storage inside the virion. Here, we used cryo-electron microscopy to determine accurate three-dimensional structure for several different assemblies of the Nipah virus nucleocapsid protein, in particular a detailed structure for the complex of this protein with RNA. This structural information is important for understanding detailed molecular interactions driving and stabilizing the nucleocapsid assembly formation that are of fundamental importance for understanding similar processes in a large group of ssRNA viruses. Apart from highlighting structural similarities and differences with nucleocapsid proteins of other viruses of the Paramyxoviridae family, these data will inform the development of new antiviral approaches for the henipaviruses.
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Affiliation(s)
- De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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8
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Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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9
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Ge M, Molt RW, Jenkins HT, Blackburn GM, Jin Y, Antson AA. Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor. ACS Catal 2021; 11:2769-2773. [PMID: 33717640 PMCID: PMC7944477 DOI: 10.1021/acscatal.0c04500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/26/2020] [Indexed: 01/11/2023]
Abstract
![]()
Isoelectronic metal
fluoride transition state analogue (TSA) complexes,
MgF3– and AlF4–, have proven to be immensely useful in understanding mechanisms
of biological motors utilizing phosphoryl transfer. Here we report
a previously unobserved octahedral TSA complex, MgF3(H2O)−, in a 1.5 Å resolution Zika virus
NS3 helicase crystal structure. 19F NMR provided independent
validation and also the direct observation of conformational tightening
resulting from ssRNA binding in solution. The TSA stabilizes the two
conformations of motif V of the helicase that link ATP hydrolysis
with mechanical work. DFT analysis further validated the MgF3(H2O)− species, indicating the significance
of this TSA for studies of biological motors.
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Affiliation(s)
- Mengyu Ge
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - Robert W. Molt
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, United States
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Yi Jin
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
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10
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Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, López-Camacho C, Slon-Campos J, Zhao Y, Stuart DI, Paesen GC, Grimes JM, Antson AA, Bayfield OW, Hawkins DEDP, Ker DS, Wang B, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler BM, Fry JW, Schwabe NF, Semple MG, Baillie JK, Moore SC, Openshaw PJM, Ansari MA, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Zhang Y, Jing R, Ho LP, Cornall RJ, Conlon CP, Klenerman P, Screaton GR, Mongkolsapaya J, McMichael A, Knight JC, Ogg G, Dong T. Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol 2020; 21:1336-1345. [PMID: 32887977 PMCID: PMC7611020 DOI: 10.1038/s41590-020-0782-6] [Citation(s) in RCA: 834] [Impact Index Per Article: 208.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/11/2020] [Indexed: 01/08/2023]
Abstract
The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4+ and/or CD8+ epitopes, including six immunodominant regions. Six optimized CD8+ epitopes were defined, with peptide-MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8+ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.
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Affiliation(s)
- Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Xuan Yao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Xinjiang, China
| | | | - Timothy Rostron
- Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David I Stuart
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Didcot, UK
| | - Guido C Paesen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan M Grimes
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Didcot, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lance Turtle
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Krishanthi Subramaniam
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paul Thomson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ping Zhang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan de Silva
- The Florey Institute for Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Paul Sopp
- Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Ushani Rajapaksa
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yi-Ling Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Wayne Paes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Benedikt M Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Institute in The Park, Alder Hey Children's Hospital, Liverpool, UK
| | - J Kenneth Baillie
- Anaesthesia, Critical Care and Pain Medicine Division of Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - M Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Georgina Kerr
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Goulder
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Teresa Lockett
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Yonghong Zhang
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ronghua Jing
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ling-Pei Ho
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Richard J Cornall
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christopher P Conlon
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Gavin R Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Andrew McMichael
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Knight
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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11
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Tugaeva KV, Titterington J, Sotnikov DV, Maksimov EG, Antson AA, Sluchanko NN. Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14‐3‐3 protein family. FEBS J 2020; 287:3944-3966. [DOI: 10.1111/febs.15474] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Kristina V. Tugaeva
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biochemistry School of Biology M.V. Lomonosov Moscow State University Russia
| | - James Titterington
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Dmitriy V. Sotnikov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
| | - Eugene G. Maksimov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
| | - Alfred A. Antson
- York Structural Biology Laboratory Department of Chemistry University of York UK
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry Moscow Russia
- Department of Biophysics School of Biology M.V. Lomonosov Moscow State University Russia
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12
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Bayfield OW, Steven AC, Antson AA. Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss. eLife 2020; 9:55517. [PMID: 32286226 PMCID: PMC7234808 DOI: 10.7554/elife.55517] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023] Open
Abstract
The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determined in situ in its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion of the conformation of the loops that define the constriction in the central tunnel, accompanied by a hydrophilic–hydrophobic switch. The structure also shows how translocation of DNA into the capsid could be modulated by a changing mode of protein–protein interactions between portal and capsid, across a symmetry-mismatched interface.
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Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.,Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
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13
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Dehghani-Tafti S, Levdikov V, Antson AA, Bax B, Sanders CM. Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Nucleic Acids Res 2019; 47:3208-3222. [PMID: 30698796 PMCID: PMC6451128 DOI: 10.1093/nar/gkz028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 01/06/2023] Open
Abstract
Pif1 is a multifunctional helicase and DNA processing enzyme that has roles in genome stability. The enzyme is conserved in eukaryotes and also found in some prokaryotes. The functions of human PIF1 (hPIF1) are also critical for survival of certain tumour cell lines during replication stress, making it an important target for cancer therapy. Crystal structures of hPIF1 presented here explore structural events along the chemical reaction coordinate of ATP hydrolysis at an unprecedented level of detail. The structures for the apo as well as the ground and transition states reveal conformational adjustments in defined protein segments that can trigger larger domain movements required for helicase action. Comparisons with the structures of yeast and bacterial Pif1 reveal a conserved ssDNA binding channel in hPIF1 that we show is critical for single-stranded DNA binding during unwinding, but not the binding of G quadruplex DNA. Mutational analysis suggests that while the ssDNA-binding channel is important for helicase activity, it is not used in DNA annealing. Structural differences, in particular in the DNA strand separation wedge region, highlight significant evolutionary divergence of the human PIF1 protein from bacterial and yeast orthologues.
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Affiliation(s)
- Saba Dehghani-Tafti
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
| | - Vladimir Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Ben Bax
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
- Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Cyril M Sanders
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
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14
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Cressiot B, Greive SJ, Mojtabavi M, Antson AA, Wanunu M. Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors. Nat Commun 2018; 9:4652. [PMID: 30405123 PMCID: PMC6220183 DOI: 10.1038/s41467-018-07116-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopore-based sensors are advancing the sensitivity and selectivity of single-molecule detection in molecular medicine and biotechnology. Current electrical sensing devices are based on either membrane protein pores supported in planar lipid bilayers or solid-state (SS) pores fabricated in thin metallic membranes. While both types of nanosensors have been used in a variety of applications, each has inherent disadvantages that limit its use. Hybrid nanopores, consisting of a protein pore supported within a SS membrane, combine the robust nature of SS membranes with the precise and simple engineering of protein nanopores. We demonstrate here a novel lipid-free hybrid nanopore comprising a natural DNA pore from a thermostable virus, electrokinetically inserted into a larger nanopore supported in a silicon nitride membrane. The hybrid pore is stable and easy to fabricate, and, most importantly, exhibits low peripheral leakage allowing sensing and discrimination among different types of biomolecules.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.,LAMBE, Université d'Evry Val d'Essonne, Université de Cergy Pontoise, CNRS, CEA, Université Paris-Saclay, Evry, F-91025, France
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
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15
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Xu RG, Jenkins HT, Antson AA, Greive SJ. Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis. Nucleic Acids Res 2018; 45:13029-13042. [PMID: 29069443 PMCID: PMC5727402 DOI: 10.1093/nar/gkx947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/13/2017] [Indexed: 11/23/2022] Open
Abstract
The crystal structure of the large terminase from the Geobacillus stearothermophilus bacteriophage D6E shows a unique relative orientation of the N-terminal adenosine triphosphatase (ATPase) and C-terminal nuclease domains. This monomeric ‘initiation’ state with the two domains ‘locked’ together is stabilized via a conserved C-terminal arm, which may interact with the portal protein during motor assembly, as predicted for several bacteriophages. Further work supports the formation of an active oligomeric state: (i) AUC data demonstrate the presence of oligomers; (ii) mutational analysis reveals a trans-arginine finger, R158, indispensable for ATP hydrolysis; (iii) the location of this arginine is conserved with the HerA/FtsK ATPase superfamily; (iv) a molecular docking model of the pentamer is compatible with the location of the identified arginine finger. However, this pentameric model is structurally incompatible with the monomeric ‘initiation’ state and is supported by the observed increase in kcat of ATP hydrolysis, from 7.8 ± 0.1 min−1 to 457.7 ± 9.2 min−1 upon removal of the C-terminal nuclease domain. Taken together, these structural, biophysical and biochemical data suggest a model where transition from the ‘initiation’ state into a catalytically competent pentameric state, is accompanied by substantial domain rearrangements, triggered by the removal of the C-terminal arm from the ATPase active site.
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Affiliation(s)
- Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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16
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Cressiot B, Greive SJ, Si W, Pascoa TC, Mojtabavi M, Chechik M, Jenkins HT, Lu X, Zhang K, Aksimentiev A, Antson AA, Wanunu M. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. ACS Nano 2017; 11:11931-11945. [PMID: 29120602 PMCID: PMC5963890 DOI: 10.1021/acsnano.7b06980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein's insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal's DNA-ratchet function.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Wei Si
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Tomas C. Pascoa
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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17
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Sluchanko NN, Tugaeva KV, Greive SJ, Antson AA. Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners. Sci Rep 2017; 7:12014. [PMID: 28931924 PMCID: PMC5607241 DOI: 10.1038/s41598-017-12214-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, several “hub” proteins integrate signals from different interacting partners that bind through intrinsically disordered regions. The 14-3-3 protein hub, which plays wide-ranging roles in cellular processes, has been linked to numerous human disorders and is a promising target for therapeutic intervention. Partner proteins usually bind via insertion of a phosphopeptide into an amphipathic groove of 14-3-3. Structural plasticity in the groove generates promiscuity allowing accommodation of hundreds of different partners. So far, accurate structural information has been derived for only a few 14-3-3 complexes with phosphopeptide-containing proteins and a variety of complexes with short synthetic peptides. To further advance structural studies, here we propose a novel approach based on fusing 14-3-3 proteins with the target partner peptide sequences. Such chimeric proteins are easy to design, express, purify and crystallize. Peptide attachment to the C terminus of 14-3-3 via an optimal linker allows its phosphorylation by protein kinase A during bacterial co-expression and subsequent binding at the amphipathic groove. Crystal structures of 14-3-3 chimeras with three different peptides provide detailed structural information on peptide-14-3-3 interactions. This simple but powerful approach, employing chimeric proteins, can reinvigorate studies of 14-3-3/phosphoprotein assemblies, including those with challenging low-affinity partners, and may facilitate the design of novel biosensors.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071, Moscow, Russian Federation. .,Department of biophysics, School of Biology, Moscow State University, 119991, Moscow, Russian Federation.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.,Department of biochemistry, School of Biology, Moscow State University, 119991, Moscow, Russian Federation
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
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18
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Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA. Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Nucleic Acids Res 2017; 45:3580-3590. [PMID: 28100693 PMCID: PMC5389553 DOI: 10.1093/nar/gkw1354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+. High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.
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Affiliation(s)
- Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Elena V Blagova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Anna Lopatina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Evgeny Klimuk
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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19
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Peters DT, Fung HKH, Levdikov VM, Irmscher T, Warrander FC, Greive SJ, Kovalevskiy O, Isaacs HV, Coles M, Antson AA. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363. Biochemistry 2016; 55:5021-7. [PMID: 27559824 PMCID: PMC5193468 DOI: 10.1021/acs.biochem.6b00682] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein-RNA complex are unknown. Characterization of human Lin28's interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions.
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Affiliation(s)
- Daniel T Peters
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom.,Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Vladimir M Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Tobias Irmscher
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Fiona C Warrander
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Oleg Kovalevskiy
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Harry V Isaacs
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Mark Coles
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
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20
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Jenkins HT, Antson AA. Fragon - rapid fragment-based molecular replacement. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022]
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
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Affiliation(s)
- Charles S Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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22
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Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
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Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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23
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Warrander F, Faas L, Kovalevskiy O, Peters D, Coles M, Antson AA, Genever P, Isaacs HV. lin28 proteins promote expression of 17∼92 family miRNAs during amphibian development. Dev Dyn 2015; 245:34-46. [PMID: 26447465 PMCID: PMC4982076 DOI: 10.1002/dvdy.24358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 12/13/2022] Open
Abstract
Background: Lin28 proteins are post‐transcriptional regulators of gene expression with multiple roles in development and the regulation of pluripotency in stem cells. Much attention has focussed on Lin28 proteins as negative regulators of let‐7 miRNA biogenesis; a function that is conserved in several animal groups and in multiple processes. However, there is increasing evidence that Lin28 proteins have additional roles, distinct from regulation of let‐7 abundance. We have previously demonstrated that lin28 proteins have functions associated with the regulation of early cell lineage specification in Xenopus embryos, independent of a lin28/let‐7 regulatory axis. However, the nature of lin28 targets in Xenopus development remains obscure. Results: Here, we show that mir‐17∼92 and mir‐106∼363 cluster miRNAs are down‐regulated in response to lin28 knockdown, and RNAs from these clusters are co‐expressed with lin28 genes during germ layer specification. Mature miRNAs derived from pre‐mir‐363 are most sensitive to lin28 inhibition. We demonstrate that lin28a binds to the terminal loop of pre‐mir‐363 with an affinity similar to that of let‐7, and that this high affinity interaction requires to conserved a GGAG motif. Conclusions: Our data suggest a novel function for amphibian lin28 proteins as positive regulators of mir‐17∼92 family miRNAs. Developmental Dynamics 245:34–46, 2016. © 2015 Wiley Periodicals, Inc. We show that mir‐17∼92 and mir‐106∼363 cluster miRNAs are down regulated in response to lin28 knockdown in Xenopus embryos. We demonstrate that lin28a binds to the terminal loop of pre‐mir‐363 and this interaction requires a conserved a GGAG motif.
Our data suggest a novel function for amphibian lin28 proteins as positive regulators of mir‐17∼92 family miRNAs.
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Affiliation(s)
- Fiona Warrander
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Laura Faas
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Oleg Kovalevskiy
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Daniel Peters
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Mark Coles
- Centre for Immunology and Infection, University of York, Heslington York, YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Paul Genever
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Harry V Isaacs
- Department of Biology, University of York, York, YO10 5DD, UK
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24
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Jenkins HT, Antson AA. A nuclease cut three ways: phasing from distant homologues, an ideal α-helix and Zn-SAD. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315097065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Bury CS, McGeehan JE, Shevtsov MB, Antson AA, Garman EF. Radiation damage in protein-nucleic acid complexes. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Whelan F, Jenkins HT, Griffiths SC, Byrne RT, Dodson EJ, Antson AA. From bacterial to human dihydrouridine synthase: automated structure determination. Acta Crystallogr D Biol Crystallogr 2015; 71:1564-71. [PMID: 26143927 PMCID: PMC4498606 DOI: 10.1107/s1399004715009220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/14/2015] [Indexed: 11/10/2022]
Abstract
The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1-340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain-domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.
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Affiliation(s)
- Fiona Whelan
- Department of Biology, The University of York, Heslington, York YO10 5DD, England
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
| | - Samuel C. Griffiths
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, England
| | - Robert T. Byrne
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Eleanor J. Dodson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
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27
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Moor NA, Vasil'eva IA, Anarbaev RO, Antson AA, Lavrik OI. Quantitative characterization of protein-protein complexes involved in base excision DNA repair. Nucleic Acids Res 2015; 43:6009-22. [PMID: 26013813 PMCID: PMC4499159 DOI: 10.1093/nar/gkv569] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 05/18/2015] [Indexed: 01/29/2023] Open
Abstract
Base Excision Repair (BER) efficiently corrects the most common types of DNA damage in mammalian cells. Step-by-step coordination of BER is facilitated by multiple interactions between enzymes and accessory proteins involved. Here we characterize quantitatively a number of complexes formed by DNA polymerase β (Polβ), apurinic/apyrimidinic endonuclease 1 (APE1), poly(ADP-ribose) polymerase 1 (PARP1), X-ray repair cross-complementing protein 1 (XRCC1) and tyrosyl-DNA phosphodiesterase 1 (TDP1), using fluorescence- and light scattering-based techniques. Direct physical interactions between the APE1-Polβ, APE1-TDP1, APE1-PARP1 and Polβ-TDP1 pairs have been detected and characterized for the first time. The combined results provide strong evidence that the most stable complex is formed between XRCC1 and Polβ. Model DNA intermediates of BER are shown to induce significant rearrangement of the Polβ complexes with XRCC1 and PARP1, while having no detectable influence on the protein–protein binding affinities. The strength of APE1 interaction with Polβ, XRCC1 and PARP1 is revealed to be modulated by BER intermediates to different extents, depending on the type of DNA damage. The affinity of APE1 for Polβ is higher in the complex with abasic site-containing DNA than after the APE1-catalyzed incision. Our findings advance understanding of the molecular mechanisms underlying coordination and regulation of the BER process.
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Affiliation(s)
- Nina A Moor
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Rashid O Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alfred A Antson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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28
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Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA. Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases. Proc Natl Acad Sci U S A 2015; 112:6033-7. [PMID: 25902496 PMCID: PMC4434734 DOI: 10.1073/pnas.1500161112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center of all Dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotides exposed at spatially distinct faces of tRNA can be accommodated in the same active site. We show that the Escherichia coli DusC is specific toward U16 of tRNA. Unexpectedly, crystal structures of DusC complexes with tRNA(Phe) and tRNA(Trp) show that Dus subfamilies that selectively modify U16 or U20 in tRNA adopt identical folds but bind their respective tRNA substrates in an almost reverse orientation that differs by a 160° rotation. The tRNA docking orientation appears to be guided by subfamily-specific clusters of amino acids ("binding signatures") together with differences in the shape of the positively charged tRNA-binding surfaces. tRNA orientations are further constrained by positional differences between the C-terminal "recognition" domains. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Daniel T Peters
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Fiona Whelan
- York Structural Biology Laboratory, Department of Chemistry, and
| | - James Stowell
- York Structural Biology Laboratory, Department of Chemistry, and Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Naveed Aziz
- Department of Biology, University of York, York, YO10 5DD, United Kingdom; Genome Canada, Ottawa, ON K2P 1P1, Canada
| | - Pavel Kasatsky
- Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute," 188300 Gatchina, Russia; St. Petersburg State Polytechnic University, 195251 St. Petersburg, Russia
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; and
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Andrey L Konevega
- Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute," 188300 Gatchina, Russia; St. Petersburg State Polytechnic University, 195251 St. Petersburg, Russia; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; and
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, and
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29
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Williams LS, Levdikov VM, Minakhin L, Severinov K, Antson AA. 12-Fold symmetry of the putative portal protein from the Thermus thermophilus bacteriophage G20C determined by X-ray analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1239-41. [PMID: 24192358 PMCID: PMC3818042 DOI: 10.1107/s174430911302486x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/05/2013] [Indexed: 08/29/2023]
Abstract
Crystal data on a putative portal protein from the thermostable bacteriophage G20C indicate that it forms a 12-subunit assembly. In tailed bacteriophages and several animal viruses, the portal protein forms the gateway through which viral DNA is translocated into the head structure during viral particle assembly. In the mature virion the portal protein exists as a dodecamer, while recombinant portal proteins from several phages, including SPP1 and CNPH82, have been shown to form 13-subunit assemblies. A putative portal protein from the thermostable bacteriophage G20C has been cloned, overexpressed and purified. Crystals of the protein diffracted to 2.1 Å resolution and belonged to space group P4212, with unit-cell parameters a = b = 155.3, c = 115.4 Å. The unit-cell content and self-rotation function calculations indicate that the protein forms a circular 12-subunit assembly.
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Affiliation(s)
- Lowri S Williams
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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30
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Loredo-Varela J, Chechik M, Levdikov VM, Abd-El-Aziz A, Minakhin L, Severinov K, Smits C, Antson AA. The putative small terminase from the thermophilic dsDNA bacteriophage G20C is a nine-subunit oligomer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:876-9. [PMID: 23908032 PMCID: PMC3729163 DOI: 10.1107/s1744309113017016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/19/2013] [Indexed: 12/04/2022]
Abstract
The putative small terminase protein from the thermostable bacteriophage G20C has been produced, purified and crystallized. The assembly of double-stranded DNA bacteriophages is dependent on a small terminase protein that normally plays two important roles. Firstly, the small terminase protein specifically recognizes viral DNA and recruits the large terminase protein, which makes the initial cut in the dsDNA. Secondly, once the complex of the small terminase, the large terminase and the DNA has docked to the portal protein, and DNA translocation into a preformed empty procapsid has begun, the small terminase modulates the ATPase activity of the large terminase. Here, the putative small terminase protein from the thermostable bacteriophage G20C, which infects the Gram-negative eubacterium Thermus thermophilus, has been produced, purified and crystallized. Size-exclusion chromatography–multi-angle laser light scattering data indicate that the protein forms oligomers containing nine subunits. Crystals diffracting to 2.8 Å resolution have been obtained. These belonged to space group P212121, with unit-cell parameters a = 94.31, b = 125.6, c = 162.8 Å. The self-rotation function and Matthews coefficient calculations are consistent with the presence of a nine-subunit oligomer in the asymmetric unit.
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Affiliation(s)
- Juan Loredo-Varela
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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31
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Byrne RT, Whelan F, Aller P, Bird LE, Dowle A, Lobley CMC, Reddivari Y, Nettleship JE, Owens RJ, Antson AA, Waterman DG. S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. Acta Crystallogr D Biol Crystallogr 2013; 69:1090-8. [PMID: 23695253 PMCID: PMC3663124 DOI: 10.1107/s0907444913004939] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 02/20/2013] [Indexed: 02/02/2023]
Abstract
The putative methyltransferase CmoA is involved in the nucleoside modification of transfer RNA. X-ray crystallography and mass spectrometry are used to show that it contains a novel SAM derivative, S-adenosyl-S-carboxymethyl-l-homocysteine, in which the donor methyl group is replaced by a carboxymethyl group. Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo5U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo5U and was annotated as an S-adenosyl-l-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel cofactor, S-adenosyl-S-carboxymethyl-l-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-ray structure, PDB entry 1im8, suggests that the active site contains SCM-SAH and not SAM.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, England
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32
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Luan W, Fesseler J, Chechik M, Buttner CR, Antson AA, Smits C. Recombinant portal protein from Staphylococcus epidermidis bacteriophage CNPH82 is a 13-subunit oligomer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1267-70. [PMID: 23027764 PMCID: PMC3490468 DOI: 10.1107/s1744309112037645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 08/31/2012] [Indexed: 11/13/2022]
Abstract
The portal protein cn3 of bacteriophage CNPH82 is predicted to serve as a gateway for translocation of viral genome into preformed pro-capsid, like portal proteins from other double-stranded DNA tailed bacteriophages. The host of bacteriophage CNPH82 is the opportunistic human pathogenic bacterium Staphylococcus epidermidis, a major cause of nosocomial infections. The portal protein of this phage has been cloned, overexpressed and purified. Size-exclusion chromatography-multi-angle laser light scattering analysis has indicated that the portal protein contains ∼13 subunits. Crystals of the portal protein, diffracting to 4.2 Å, have been obtained. These crystals belong to the space group C222(1) with the unit-cell parameters of a = 252.4, b = 367.0, c = 175.5 Å. The self-rotation function revealed the presence of a single 13-subunit oligomer in the asymmetric unit.
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Affiliation(s)
- Weisha Luan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Jochen Fesseler
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Carina R. Buttner
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Callum Smits
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
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Sluchanko NN, Artemova NV, Sudnitsyna MV, Safenkova IV, Antson AA, Levitsky DI, Gusev NB. Monomeric 14-3-3ζ has a chaperone-like activity and is stabilized by phosphorylated HspB6. Biochemistry 2012; 51:6127-38. [PMID: 22794279 PMCID: PMC3413243 DOI: 10.1021/bi300674e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Members of the 14-3-3 eukaryotic protein family predominantly
function
as dimers. The dimeric form can be converted into monomers upon phosphorylation
of Ser58 located at the subunit interface. Monomers are
less stable than dimers and have been considered to be either less
active or even inactive during binding and regulation of phosphorylated
client proteins. However, like dimers, monomers contain the phosphoserine-binding
site and therefore can retain some functions of the dimeric 14-3-3.
Furthermore, 14-3-3 monomers may possess additional functional roles
owing to their exposed intersubunit surfaces. Previously we have found
that the monomeric mutant of 14-3-3ζ (14-3-3ζm), like the wild type protein, is able to bind phosphorylated small
heat shock protein HspB6 (pHspB6), which is involved in the regulation
of smooth muscle contraction and cardioprotection. Here we report
characterization of the 14-3-3ζm/pHspB6 complex by
biophysical and biochemical techniques. We find that formation of
the complex retards proteolytic degradation and increases thermal
stability of the monomeric 14-3-3, indicating that interaction with
phosphorylated targets could be a general mechanism of 14-3-3 monomers
stabilization. Furthermore, by using myosin subfragment 1 (S1) as
a model substrate we find that the monomer has significantly higher
chaperone-like activity than either the dimeric 14-3-3ζ protein
or even HspB6 itself. These observations indicate that 14-3-3ζ
and possibly other 14-3-3 isoforms may have additional functional
roles conducted by the monomeric state.
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Affiliation(s)
- Nikolai N Sluchanko
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russian Federation.
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Whelan F, Stead JA, Shkumatov AV, Svergun DI, Sanders CM, Antson AA. A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding. Nucleic Acids Res 2012; 40:2271-83. [PMID: 22067453 PMCID: PMC3300016 DOI: 10.1093/nar/gkr906] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 09/27/2011] [Accepted: 10/06/2011] [Indexed: 11/26/2022] Open
Abstract
The mechanism of DNA translocation by papillomavirus E1 and polyomavirus LTag hexameric helicases involves consecutive remodelling of subunit-subunit interactions around the hexameric ring. Our biochemical analysis of E1 helicase demonstrates that a 26-residue C-terminal segment is critical for maintaining the hexameric assembly. As this segment was not resolved in previous crystallographic analysis of E1 and LTag hexameric helicases, we determined the solution structure of the intact hexameric E1 helicase by Small Angle X-ray Scattering. We find that the C-terminal segment is flexible and occupies a cleft between adjacent subunits in the ring. Electrostatic potential calculations indicate that the negatively charged C-terminus can bridge the positive electrostatic potentials of adjacent subunits. Our observations support a model in which the C-terminal peptide serves as a flexible 'brace' maintaining the oligomeric state during conformational changes associated with ATP hydrolysis. We argue that these interactions impart processivity to DNA unwinding. Sequence and disorder analysis suggest that this mechanism of hexamer stabilization would be conserved among papillomavirus E1 and polyomavirus LTag hexameric helicases.
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Affiliation(s)
- Fiona Whelan
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
| | - Jonathan A. Stead
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
| | - Alexander V. Shkumatov
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
| | - Dmitri I. Svergun
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
| | - Cyril M. Sanders
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
| | - Alfred A. Antson
- York Structural Biology Laboratory, The University of York, York YO10 5DD, Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, Geb 25 A, 22603 Hamburg, Germany
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Griffiths S, Byrne RT, Antson AA, Whelan F. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:333-6. [PMID: 22442237 DOI: 10.1107/s1744309112003831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/29/2012] [Indexed: 11/11/2022]
Abstract
Dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the D-loop and variable loop of tRNA. The human dihydrouridine synthase HsDus2L has been implicated in the development of pulmonary carcinogenesis. Here, the purification, crystallization and preliminary X-ray characterization of the HsDus2L catalytic domain are reported. The crystals belonged to space group P2(1) and contained a single molecule of HsDus2L in the asymmetric unit. A complete data set was collected to 1.9 Å resolution using synchrotron radiation.
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Affiliation(s)
- Sam Griffiths
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, England
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36
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Milić D, V. Demidkina T, N. Zakomirdina L, Matković-Čalogović D, A. Antson A. Crystal Structure of Citrobacter freundii Asp214Ala Tyrosine Phenollyase Reveals that Asp214 is Critical for Maintaining a Strain in the Internal Aldimine. CROAT CHEM ACTA 2012. [DOI: 10.5562/cca1915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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37
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Sluchanko NN, Sudnitsyna MV, Seit-Nebi AS, Antson AA, Gusev NB. Properties of the monomeric form of human 14-3-3ζ protein and its interaction with tau and HspB6. Biochemistry 2011; 50:9797-808. [PMID: 21978388 DOI: 10.1021/bi201374s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dimers formed by seven isoforms of the human 14-3-3 protein participate in multiple cellular processes. The dimeric form has been extensively characterized; however, little is known about the structure and properties of the monomeric form of 14-3-3. The monomeric form is involved in the assembly of homo- and heterodimers, which could partially dissociate back into monomers in response to phosphorylation at Ser58. To obtain monomeric forms of human 14-3-3ζ, we produced four protein constructs with different combinations of mutated (M) or wild-type (W) segments E(5), (12)LAE(14), and (82)YREKIE(87). Under a wide range of expression conditions in Escherichia coli, the MMM and WMM mutants were insoluble, whereas WMW and MMW mutants were soluble, highly expressed, and purified to homogeneity. WMW and MMW mutants remained monomeric over a wide range of concentrations while retaining the α-helical structure characteristic of wild-type 14-3-3. However, WMW and MMW mutants were highly susceptible to proteolysis and had much lower thermal stabilities than the wild-type protein. Using WMW and MMW mutants, we show that the monomeric form interacts with the tau protein and with the HspB6 protein, in both cases forming complexes with a 1:1 stoichiometry, in contrast to the 2:1 and/or 2:2 complexes formed by wild-type 14-3-3. Significantly, this interaction requires phosphorylation of tau protein and HspB6. Because of minimal changes in structure, MMW and especially WMW mutant proteins are promising candidates for analyzing the effect of monomerization on the physiologically important properties of 14-3-3ζ.
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Affiliation(s)
- Nikolai N Sluchanko
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation
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38
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Milić D, Demidkina TV, Faleev NG, Phillips RS, Matković-Čalogović D, Antson AA. Crystallographic snapshots of tyrosine phenol-lyase show that substrate strain plays a role in C-C bond cleavage. J Am Chem Soc 2011; 133:16468-76. [PMID: 21899319 PMCID: PMC3191766 DOI: 10.1021/ja203361g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 11/30/2022]
Abstract
The key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cβ-Cγ bond of L-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon-carbon bond. As for most other pyridoxal 5'-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-L-tyrosine followed by flash-cooling. The X-ray structures, determined at ~2.0 Å resolution, reveal two quinonoid geometries: "relaxed" in the open and "tense" in the closed state of the active site. The "tense" state is characterized by changes in enzyme contacts made with the substrate's phenolic moiety, which result in significantly strained conformation at Cβ and Cγ positions. We also captured, at 2.25 Å resolution, the X-ray structure for the state just after the substrate's Cβ-Cγ bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the α-aminoacrylate intermediate with bound phenol. In this state, the enzyme-ligand contacts remain almost exactly the same as in the "tense" quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state.
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Affiliation(s)
- Dalibor Milić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Tatyana V. Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Nicolai G. Faleev
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Street, Moscow 119991, Russia
| | - Robert S. Phillips
- Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Dubravka Matković-Čalogović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Alfred A. Antson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
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Chen CS, Smits C, Dodson GG, Shevtsov MB, Merlino N, Gollnick P, Antson AA. How to change the oligomeric state of a circular protein assembly: switch from 11-subunit to 12-subunit TRAP suggests a general mechanism. PLoS One 2011; 6:e25296. [PMID: 21984911 PMCID: PMC3184956 DOI: 10.1371/journal.pone.0025296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 08/31/2011] [Indexed: 11/24/2022] Open
Abstract
Background Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated. Methodology/Principal Findings We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data. Conclusions/Significance The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states.
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Affiliation(s)
- Chao-Sheng Chen
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Callum Smits
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Guy G. Dodson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Mikhail B. Shevtsov
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- Biological Sciences, University of Portsmouth, King Henry Building, Portsmouth, United Kingdom
| | - Natalie Merlino
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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40
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Silva APG, Chechik M, Byrne RT, Waterman DG, Ng CL, Dodson EJ, Koonin EV, Antson AA, Smits C. Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. Structure 2011; 19:622-32. [PMID: 21565697 PMCID: PMC3095777 DOI: 10.1016/j.str.2011.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 03/03/2011] [Accepted: 03/09/2011] [Indexed: 11/03/2022]
Abstract
MTH1203, a β-CASP metallo-β-lactamase family nuclease from the archaeon Methanothermobacter thermautotrophicus, was identified as a putative nuclease that might contribute to RNA processing. The crystal structure of MTH1203 reveals that, in addition to the metallo-β-lactamase nuclease and the β-CASP domains, it contains two contiguous KH domains that are unique to MTH1203 and its orthologs. RNA-binding experiments indicate that MTH1203 preferentially binds U-rich sequences with a dissociation constant in the micromolar range. In vitro nuclease activity assays demonstrated that MTH1203 is a zinc-dependent nuclease. MTH1203 is also shown to be a dimer and, significantly, this dimerization enhances the nuclease activity. Transcription termination in archaea produces mRNA transcripts with U-rich 3' ends that could be degraded by MTH1203 considering its RNA-binding specificity. We hypothesize that this nuclease degrades mRNAs of proteins targeted for degradation and so regulates archaeal RNA turnover, possibly in concert with the exosome.
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Affiliation(s)
- Ana P G Silva
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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41
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Milić D, Demidkina TV, Matković-Čalogović D, Antson AA. Asp214→Ala mutation reorganizes the active site of Citrobacter freundiityrosine phenol-lyase. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310093608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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42
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Ng CL, Waterman DG, Antson AA, Ortiz-Lombardía M. Structure of the Methanothermobacter thermautotrophicus exosome RNase PH ring. Acta Crystallogr D Biol Crystallogr 2010; 66:522-8. [PMID: 20445227 DOI: 10.1107/s0907444910002908] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 01/23/2010] [Indexed: 08/30/2023]
Abstract
The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeon Methanothermobacter thermautotrophicus is described at 2.65 A resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme.
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Affiliation(s)
- C Leong Ng
- York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, England.
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Shevtsov MB, Chen Y, Isupov MN, Leech A, Gollnick P, Antson AA. Bacillus licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers. J Struct Biol 2010; 170:127-33. [PMID: 20138150 PMCID: PMC2896485 DOI: 10.1016/j.jsb.2010.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/21/2010] [Accepted: 01/23/2010] [Indexed: 01/07/2023]
Abstract
Anti-TRAP (AT) protein regulates expression of tryptophan biosynthetic genes by binding to the trp RNA-binding attenuation protein (TRAP) and preventing its interaction with RNA. Bacillus subtilis AT forms trimers that can either interact with TRAP or can further assemble into dodecameric particles. To determine which oligomeric forms are preserved in AT proteins of other Bacilli we studied Bacillus licheniformis AT which shares 66% sequence identity with the B. subtilis protein. We show that in solution B. licheniformis AT forms stable trimers. In crystals, depending on pH, such trimers assemble into two different types of dodecameric particles, both having 23 point group symmetry. The dodecamer formed at pH 6.0 has the same conformation as previously observed for B. subtilis AT. This dodecamer contains a large internal chamber with the volume of approximately 700 A(3), which is lined by the side chains of twelve valine residues. The presence of the hydrophobic chamber hints at the possibility that the dodecamer formation could be induced by binding of a ligand. Interestingly, in the dodecamer formed at pH 8.0 all trimers are turned inside out relatively to the form observed at pH 6.0.
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Affiliation(s)
- Mikhail B. Shevtsov
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO1 5YW, UK
| | - Yanling Chen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Michail N. Isupov
- School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Leech
- Department of Biology, University of York, Heslington, York YO1 5DD, UK
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO1 5YW, UK,Corresponding author. Fax: +44 1904 328266.
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Abstract
Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNAPhe from Escherichia coli at a resolution of 3 Å. We show that in the absence of modifications the overall fold of the tRNA is essentially the same as that of mature tRNA. However, there are a number of significant structural differences, such as rearrangements in a triplet base pair and a widened angle between the acceptor and anticodon stems. Contrary to previous observations, the anticodon adopts the same conformation as seen in mature tRNA.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, North Yorkshire, YO10 5YW, UK
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45
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Kovalevskiy OV, Solonin AS, Antson AA. Structural investigation of transcriptional regulator HlyIIR: Influence of a disordered region on protein fold and dimerization. Proteins 2010; 78:1870-7. [DOI: 10.1002/prot.22700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Ng CL, Waterman DG, Koonin EV, Walters AD, Chong JPJ, Isupov MN, Lebedev AA, Bunka DHJ, Stockley PG, Ortiz-Lombardía M, Antson AA. Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein. BMC Struct Biol 2009; 9:32. [PMID: 19454024 PMCID: PMC2695463 DOI: 10.1186/1472-6807-9-32] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 05/19/2009] [Indexed: 01/06/2023]
Abstract
Background Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown. Results We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner. Conclusion It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function.
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Affiliation(s)
- C Leong Ng
- York Structural Biology Laboratory, Chemistry Department, University of York, York, YO10 5YW, UK.
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Kovalevskiĭ OV, Antson AA, Solonin AS. [Contraction of the disordered loop located within C-terminal domain of the transcriptional regulator HlyIIR causes its structural rearrangement]. Mol Biol (Mosk) 2009; 43:126-135. [PMID: 19334535 PMCID: PMC3145143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
HlyIIR is a negative transcriptional regulator of the hemolysin II gene from Bacillus cereus. A disordered region (amino acid residues 170-185) localized within the C-terminal domain near the dimerization interface was found in the recently determined HlyIIR X-ray structure. To clarify the effect of this region on HlyIIR properties and potential improvement of the diffraction quality of its crystals, we constructed a HlyIIR mutant with a single alanine residue substituting for the overall disordered region. According to biochemical analysis, the mutant protein still formed a dimer but lost its DNA-binding activity. Its crystals displayed better diffraction quality as compared with the native protein. The mutant structure was determined by X-ray analysis with a resolution of 2.1 Å. However, the mutant protein formed an alternative dimer differing from the wild-type dimer, as its subunits were rotated by 160. The conformation of individual subunits also partially changed. As this considerable remodeling in the mutant protein structure resulted from the conformational changes in the segment Pro161-Ser169, we concluded that this segment was important for maintaining the native HlyIIR structure.
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Silva APG, Byrne RT, Chechik M, Smits C, Waterman DG, Antson AA. Expression, purification, crystallization and preliminary X-ray studies of the TAN1 orthologue from Methanothermobacter thermautotrophicus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1083-6. [PMID: 18997348 DOI: 10.1107/s1744309108034039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 10/17/2008] [Indexed: 11/10/2022]
Abstract
MTH909 is the Methanothermobacter thermautotrophicus orthologue of Saccharomyces cerevisiae TAN1, which is required for N(4)-acetylcytidine formation in tRNA. The protein consists of an N-terminal near-ferredoxin-like domain and a C-terminal THUMP domain. Unlike most other proteins containing the THUMP domain, TAN1 lacks any catalytic domains and has been proposed to form a complex with a catalytic protein that is capable of making base modifications. MTH909 has been cloned, overexpressed and purified. The molecule exists as a monomer in solution. X-ray data were collected to 2.85 A resolution from a native crystal belonging to space group P6(1)22 (or P6(5)22), with unit-cell parameters a = 69.9, c = 408.5 A.
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Affiliation(s)
- Ana P G Silva
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, England
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Milić D, Demidkina TV, Faleev NG, Matković-Calogović D, Antson AA. Insights into the catalytic mechanism of tyrosine phenol-lyase from X-ray structures of quinonoid intermediates. J Biol Chem 2008; 283:29206-14. [PMID: 18715865 PMCID: PMC2662015 DOI: 10.1074/jbc.m802061200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 08/11/2008] [Indexed: 11/06/2022] Open
Abstract
Amino acid transformations catalyzed by a number of pyridoxal 5'-phosphate (PLP)-dependent enzymes involve abstraction of the Calpha proton from an external aldimine formed between a substrate and the cofactor leading to the formation of a quinonoid intermediate. Despite the key role played by the quinonoid intermediates in the catalysis by PLP-dependent enzymes, limited accurate information is available about their structures. We trapped the quinonoid intermediates of Citrobacter freundii tyrosine phenol-lyase with L-alanine and L-methionine in the crystalline state and determined their structures at 1.9- and 1.95-A resolution, respectively, by cryo-crystallography. The data reveal a network of protein-PLP-substrate interactions that stabilize the planar geometry of the quinonoid intermediate. In both structures the protein subunits are found in two conformations, open and closed, uncovering the mechanism by which binding of the substrate and restructuring of the active site during its closure protect the quinonoid intermediate from the solvent and bring catalytically important residues into positions suitable for the abstraction of phenol during the beta-elimination of L-tyrosine. In addition, the structural data indicate a mechanism for alanine racemization involving two bases, Lys-257 and a water molecule. These two bases are connected by a hydrogen bonding system allowing internal transfer of the Calpha proton.
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Affiliation(s)
- Dalibor Milić
- Laboratory of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia.
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Sanders CM, Kovalevskiy OV, Sizov D, Lebedev AA, Isupov MN, Antson AA. Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors. Nucleic Acids Res 2007; 35:6451-7. [PMID: 17881379 PMCID: PMC2095799 DOI: 10.1093/nar/gkm705] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.
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Affiliation(s)
- Cyril M. Sanders
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Oleg V. Kovalevskiy
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Dmytro Sizov
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Andrey A. Lebedev
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Michail N. Isupov
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Alfred A. Antson
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia, York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK, Taras Shevchenko Kiev State University, Biology Faculty, Virology Department, Glushkova Avenue 2, 03127 Kiev, Ukraine and Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- *To whom correspondence should be addressed. +44 1904328255+44 1904328266
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