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  • 1
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    HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-11-08
    Description: SAMHD1, an analogue of the murine interferon (IFN)-gamma-induced gene Mg11 (ref. 1), has recently been identified as a human immunodeficiency virus-1 (HIV-1) restriction factor that blocks early-stage virus replication in dendritic and other myeloid cells and is the target of the lentiviral protein Vpx, which can relieve HIV-1 restriction. SAMHD1 is also associated with Aicardi-Goutieres syndrome (AGS), an inflammatory encephalopathy characterized by chronic cerebrospinal fluid lymphocytosis and elevated levels of the antiviral cytokine IFN-alpha. The pathology associated with AGS resembles congenital viral infection, such as transplacentally acquired HIV. Here we show that human SAMHD1 is a potent dGTP-stimulated triphosphohydrolase that converts deoxynucleoside triphosphates to the constituent deoxynucleoside and inorganic triphosphate. The crystal structure of the catalytic core of SAMHD1 reveals that the protein is dimeric and indicates a molecular basis for dGTP stimulation of catalytic activity against dNTPs. We propose that SAMHD1, which is highly expressed in dendritic cells, restricts HIV-1 replication by hydrolysing the majority of cellular dNTPs, thus inhibiting reverse transcription and viral complementary DNA (cDNA) synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldstone, David C -- Ennis-Adeniran, Valerie -- Hedden, Joseph J -- Groom, Harriet C T -- Rice, Gillian I -- Christodoulou, Evangelos -- Walker, Philip A -- Kelly, Geoff -- Haire, Lesley F -- Yap, Melvyn W -- de Carvalho, Luiz Pedro S -- Stoye, Jonathan P -- Crow, Yanick J -- Taylor, Ian A -- Webb, Michelle -- MC_U117512710/Medical Research Council/United Kingdom -- MC_U117533887/Medical Research Council/United Kingdom -- MC_U117565647/Medical Research Council/United Kingdom -- MC_UP_A253_1111/Medical Research Council/United Kingdom -- U117512710/Medical Research Council/United Kingdom -- U117565647/Medical Research Council/United Kingdom -- England -- Nature. 2011 Nov 6;480(7377):379-82. doi: 10.1038/nature10623.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Structure, MRC National Institute for Medical Research, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22056990" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Dendritic Cells/metabolism/virology ; Deoxyadenine Nucleotides/metabolism ; Deoxycytosine Nucleotides/metabolism ; Deoxyguanine Nucleotides/metabolism ; HIV-1/*physiology ; Humans ; Hydrolysis ; Models, Biological ; Models, Molecular ; Monomeric GTP-Binding Proteins/*chemistry/genetics/*metabolism ; Myeloid Cells/virology ; Nucleoside-Triphosphatase/*chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Reverse Transcription ; Thymine Nucleotides/metabolism ; Viral Regulatory and Accessory Proteins/metabolism ; Virus Replication
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Structural basis of lentiviral subversion of a cellular protein degradation pathway (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-12-18
    Description: Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits human immunodeficiency virus (HIV)-1 infection of myeloid-lineage cells as well as resting CD4(+) T cells by reducing the cellular deoxynucleoside 5'-triphosphate (dNTP) concentration to a level at which the viral reverse transcriptase cannot function. In other lentiviruses, including HIV-2 and related simian immunodeficiency viruses (SIVs), SAMHD1 restriction is overcome by the action of viral accessory protein x (Vpx) or the related viral protein r (Vpr) that target and recruit SAMHD1 for proteasomal degradation. The molecular mechanism by which these viral proteins are able to usurp the host cell's ubiquitination machinery to destroy the cell's protection against these viruses has not been defined. Here we present the crystal structure of a ternary complex of Vpx with the human E3 ligase substrate adaptor DCAF1 and the carboxy-terminal region of human SAMHD1. Vpx is made up of a three-helical bundle stabilized by a zinc finger motif, and wraps tightly around the disc-shaped DCAF1 molecule to present a new molecular surface. This adapted surface is then able to recruit SAMHD1 via its C terminus, making it a competent substrate for the E3 ligase to mark for proteasomal degradation. The structure reported here provides a molecular description of how a lentiviral accessory protein is able to subvert the cell's normal protein degradation pathway to inactivate the cellular viral defence system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886899/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886899/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwefel, David -- Groom, Harriet C T -- Boucherit, Virginie C -- Christodoulou, Evangelos -- Walker, Philip A -- Stoye, Jonathan P -- Bishop, Kate N -- Taylor, Ian A -- 084955/Wellcome Trust/United Kingdom -- MC_U117512710/Medical Research Council/United Kingdom -- MC_U117565647/Medical Research Council/United Kingdom -- MC_U117592729/Medical Research Council/United Kingdom -- U117512710/Medical Research Council/United Kingdom -- U11756564/Medical Research Council/United Kingdom -- U117592729/Medical Research Council/United Kingdom -- England -- Nature. 2014 Jan 9;505(7482):234-8. doi: 10.1038/nature12815. Epub 2013 Dec 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. ; Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336198" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/*metabolism ; Cercocebus atys/virology ; Crystallography, X-Ray ; HIV/*chemistry/*physiology ; Host-Pathogen Interactions ; Humans ; Models, Molecular ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/chemistry/*metabolism ; Proteasome Endopeptidase Complex/metabolism ; *Proteolysis ; Simian Immunodeficiency Virus/chemistry/physiology ; Ubiquitination ; Viral Regulatory and Accessory Proteins/*chemistry/*metabolism ; vpr Gene Products, Human Immunodeficiency Virus/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Ordered assembly of murine leukemia virus capsid protein on lipid nanotubes directs specific binding by the restriction factor, Fv1 (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-03-21
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-24
    Description: The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB–DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2–DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2–DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB–DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Ordered assembly of murine leukemia virus capsid protein on lipid nanotubes directs specific binding by the restriction factor, Fv1 [Microbiology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-04-06
    Description: The restriction factor Fv1 confers resistance to murine leukemia virus (MLV), blocking progression of the viral life cycle after reverse transcription, but before integration into the host chromosome. It is known that the specificity of restriction is determined by both the restriction factor and the viral capsid (CA), but a direct interaction between Fv1 and MLV CA has not yet been demonstrated. With the development of a previously unexplored method for in vitro polymerization of MLV CA, it has now been possible to display a binding interaction between Fv1 and MLV CA. C-terminally His-tagged CA molecules were assembled on Ni-chelating lipid nanotubes, and analysis by electron microscopy revealed the formation of a regular lattice. Comparison of binding data with existing restriction data confirmed the specificity of the binding interaction, with multiple positions of both Fv1 and CA shown to influence binding specificity.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Structure of postentry restriction factors [Microbiology] (2014)
    National Academy of Sciences
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    Publication Date: 2014-07-02
    Description: Restriction factors (RFs) form important components of host defenses to retroviral infection. The Fv1, Trim5α, and TrimCyp RFs contain N-terminal dimerization and C-terminal specificity domains that target assembled retroviral capsid (CA) proteins enclosing the viral core. However, the molecular detail of the interaction between RFs and their CA targets is...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Assessing oxygen depletion in the Northeastern Pacific Ocean during the last deglaciation using I/Ca ratios from multiple benthic foraminiferal species (2017)
    Wiley
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    Publication Date: 2017-06-28
    Description: Paleo-redox proxies are crucial for reconstructing past bottom water oxygen concentration changes brought about by ocean circulation and marine productivity shifts in response to climate forcing. Carbonate I/Ca ratios of multiple benthic foraminifera species from ODP Hole 1017E – a core drilled within the Californian oxygen minimum zone (OMZ), on the continental slope – are employed to re-examine the transition from the well oxygenated last glacial into poorly oxygenated modern conditions. The redox and export productivity history of this site is constrained by numerous proxies, used to assess sensitivity of I/Ca ratios of benthic foraminifera to changes in bottom- and pore water O 2 concentrations. Reconstructed iodate (IO 3 - ) availability from the I/Ca ratio of epifaunal ( Cibicidoides sp.), shallow infaunal ( Uvigerina peregrina ), and deep infaunal ( Bolivina spissa ) foraminifera. The reconstructed IO 3 - availability profile is used to determine the contribution of bottom water O 2 relative to oxidant demand on pore water O 2 concentrations. These results suggest that high export productivity on the California Margin drove pore low water O 2 concentrations during the Bølling. In contrast low bottom water O 2 concentrations at 950 m water depth only contributed to reduced sediments during the Allerød. Increased contribution of modified North Pacific Intermediate Water to the California Current System ventilated the California OMZ during the late glacial and the Younger Dryas such that water overlying the site was oxygenated. These results highlight the promising potential of this new proxy for understanding the relative influence of bottom water O 2 concentration and pore water oxidant demand on OMZs.
    Print ISSN: 0883-8305
    Electronic ISSN: 1944-9186
    Topics: Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor (2006)
    Oxford University Press
    Details
    Publication Date: 2006-12-07
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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