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  • 1
    Language: English
    In: Journal of bacteriology, December 2012, Vol.194(23), pp.6622-3
    Description: Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (∼5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.
    Keywords: Genome, Bacterial ; Sequence Analysis, DNA ; DNA, Bacterial -- Chemistry ; Streptomyces -- Genetics
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 2
    Language: English
    In: Journal of bacteriology, October 2012, Vol.194(19), pp.5474-5
    Description: Here we report the draft genome sequence of a Streptomyces strain, AA1529, isolated from marine sediment from the Yellow Sea. Its genome contains a subset of unique genes and gene clusters that encode diverse secondary metabolites, suggesting great potential as a source for the discovery of novel gene clusters and bioactive compounds.
    Keywords: Genome, Bacterial ; Streptomyces -- Classification
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 3
    Language: English
    In: Science, 22 November 2010, Vol.330(11, 2010)
    Description: CCA-adding enzymes [ATP(CTP):tRNA nucleotidyltransferases] add CCA onto the 3{prime} end of transfer RNA (tRNA) precursors without using a nucleic acid template. Although the mechanism by which cytosine (C) is selected at position 75 of tRNA has been established, the mechanism by which adenine (A) is selected at position 76 remains elusive. Here, we report five cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. These structures suggest that adenosine 5{prime}-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a general base. The discrimination against incorporation of cytidine 5{prime}-triphosphate (CTP) at position 76 arises from improper placement of the {alpha} phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3{prime} hydroxyl group of cytidine75.
    Keywords: Basic Biological Sciences ; General And Miscellaneous//Mathematics, Computing, And Information Science ; Adenines ; Adenosine ; Arginine ; Cytidine ; Cytosine ; Enzymes ; Nucleic Acids ; Nucleosides ; Nucleotidyltransferases ; Phosphates ; Transfer RNA ; Sciences (General)
    ISSN: 0193-4511
    ISSN: 00368075
    E-ISSN: 10959203
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  • 4
    In: Nature, 2004, Vol.430(7000), p.640
    Description: Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. Here we describe the crystal structure of the Archaeoglobus fulgidus tRNA nucleotidyltransferase in complex with tRNA. We also present ternary complexes of this enzyme with both RNA duplex mimics of the tRNA acceptor stem that terminate with the nucleotides C74 or C75, as well as the appropriate incoming nucleoside 5'-triphosphates. A single nucleotide-binding pocket exists whose specificity for both CTP and ATP is determined by the protein side chain of Arg 224 and backbone phosphates of the tRNA, which are non-complementary to and thus exclude UTP and GTP. Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA. [PUBLICATION ]
    Keywords: Archaeoglobus Fulgidus–Enzymology ; Base Sequence–Metabolism ; Binding Sites–Genetics ; Crystallography, X-Ray–Metabolism ; Models, Molecular–Chemistry ; Nucleic Acid Conformation–Metabolism ; Nucleotides–Biosynthesis ; Oligonucleotides–Chemistry ; Oligonucleotides–Genetics ; Protein Structure, Tertiary–Metabolism ; RNA Nucleotidyltransferases–Genetics ; RNA Nucleotidyltransferases–Genetics ; RNA, Transfer, Phe–Genetics ; RNA, Transfer, Phe–Genetics ; RNA, Transfer, Phe–Genetics ; RNA, Transfer, Phe–Genetics ; Saccharomyces Cerevisiae–Genetics ; Substrate Specificity–Genetics ; Templates, Genetic–Genetics ; Ribonucleic Acid ; Enzymes ; Genes ; Ribonucleic Acid–RNA ; Nucleotides ; Oligonucleotides ; RNA, Transfer, Phe ; RNA Nucleotidyltransferases ; Trna Nucleotidyltransferase;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 5
    Language: English
    In: Journal of Molecular Biology, 20 February 2014, Vol.426(4), pp.980-993
    Description: Sharpening is a powerful method to restore the details from blurred electron density in crystals with high overall temperature factors ( -factors). This valuable technique is currently not optimally used because of the uncertainty in the scope of its application and ambiguities in practice. We performed an analysis of ~ 2000 crystal data sets deposited in the Protein Data Bank and show that sharpening improves the electron density map in many cases across all resolution ranges, often with dramatic enhancement for mid- and low-resolution structures. It is effective when used with either experimental or model phases without introducing additional bias. Our tests also provide a practical guide for optimal sharpening. We further show that anisotropic diffraction correction improves electron density in many cases but should be used with caution. Our study demonstrates that a routine practice of electron density sharpening may have a broad impact on the outcomes of structural biology studies.
    Keywords: B-Factor Sharpening ; Anisotropic Correction ; Automated Model Building ; Phase Error Tolerance ; Model-Bias Tolerance ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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  • 6
    Language: English
    In: Proc. Natl. Acad. Sci. USA, 08 November 2012, Vol.109((45) ; 11, 2012)
    Description: Tripartite motif protein isoform 5 alpha (TRIM5a) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5[alpha] recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5a induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5a PRY/ SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5[alpha] PRY/SPRY, but not the human TRIM5[alpha] PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5[alpha] that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5[alpha]-mediated retroviral restriction. doi/10.1073/pnas.1210903109
    Keywords: Hiv Infections -- Drug Therapy ; Hiv Infections -- Research ; Antiviral Agents -- Research ; Protein Structure -- Research;
    ISSN: 00278424
    E-ISSN: 10916490
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  • 7
    Language: English
    In: Journal of Biological Chemistry, 10 November 2015, Vol.290(10)
    Description: SAMHD1 is a cellular protein that plays key roles in HIV-1 restriction and regulation of cellular dNTP levels. Mutations in SAMHD1 are also implicated in the pathogenesis of chronic lymphocytic leukemia and Aicardi-Goutières syndrome. The anti-HIV-1 activity of SAMHD1 is negatively modulated by phosphorylation at residue Thr-592. The mechanism underlying the effect of phosphorylation on anti-HIV-1 activity remains unclear. SAMHD1 forms tetramers that possess deoxyribonucleotide triphosphate triphosphohydrolase (dNTPase) activity, which is allosterically controlled by the combined action of GTP and all four dNTPs. Here we demonstrate that the phosphomimetic mutation T592E reduces the stability of the SAMHD1 tetramer and the dNTPase activity of the enzyme. To better understand the underlying mechanisms, we determined the crystal structures of SAMHD1 variants T592E and T592V. Although the neutral substitution T592V does not perturb the structure, the charged T592E induces large conformational changes, likely triggered by electrostatic repulsion from a distinct negatively charged environment surrounding Thr-592. The phosphomimetic mutation results in a significant decrease in the population of active SAMHD1 tetramers, and hence the dNTPase activity is substantially decreased. These results provide a mechanistic understanding of how SAMHD1 phosphorylation at residue Thr-592 may modulate its cellular and antiviral functions.
    Keywords: Chemistry ; Anatomy & Physiology
    ISSN: 0021-9258
    E-ISSN: 1083-351X
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  • 8
    Language: English
    In: Journal of Applied Physics, 07 October 2013, Vol.114(13)
    Description: The characteristics of blue InGaN light-emitting diodes with AlGaN barriers of different step-like growth range Al composition and gradually increasing Al composition are investigated numerically. The simulation results indicate that the enhanced electron confinement and hole injection efficiency are mainly attributed to the mitigated downward band bending of the last barrier induced by polarization field, and the improved carrier distribution is owing to the increasing blocking for electrons as well as the decreasing blocking for holes. What's more, the output power, the distribution and rate of radiative recombination and the efficiency droop are markedly improved.
    Keywords: Articles
    ISSN: 0021-8979
    E-ISSN: 1089-7550
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  • 9
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 14 October 2014, Vol.111(41), pp.E4305-14
    Description: The sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a dNTPase, prevents the infection of nondividing cells by retroviruses, including HIV, by depleting the cellular dNTP pool available for viral reverse transcription. SAMHD1 is a major regulator of cellular dNTP levels in mammalian cells. Mutations in SAMHD1 are associated with chronic lymphocytic leukemia (CLL) and the autoimmune condition Aicardi Goutières syndrome (AGS). The dNTPase activity of SAMHD1 can be regulated by dGTP, with which SAMHD1 assembles into catalytically active tetramers. Here we present extensive biochemical and structural data that reveal an exquisite activation mechanism of SAMHD1 via combined action of both GTP and dNTPs. We obtained 26 crystal structures of SAMHD1 in complex with different combinations of GTP and dNTP mixtures, which depict the full spectrum of GTP/dNTP binding at the eight allosteric and four catalytic sites of the SAMHD1 tetramer. Our data demonstrate how SAMHD1 is activated by binding of GTP or dGTP at allosteric site 1 and a dNTP of any type at allosteric site 2. Our enzymatic assays further reveal a robust regulatory mechanism of SAMHD1 activity, which bares resemblance to that of the ribonuclease reductase responsible for cellular dNTP production. These results establish a complete framework for a mechanistic understanding of the important functions of SAMHD1 in the regulation of cellular dNTP levels, as well as in HIV restriction and the pathogenesis of CLL and AGS.
    Keywords: HIV Restriction Factor ; Allosteric Regulation ; Dntp Metabolism ; Tetramerization ; Triphosphohydrolase ; Monomeric Gtp-Binding Proteins -- Chemistry ; Nucleotides -- Chemistry
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 10
    Language: English
    In: Journal of molecular biology, 03 February 2012, Vol.415(5), pp.866-80
    Description: Human immunodeficiency virus type 1 (HIV-1) requires reverse transcriptase (RT) and HIV-1 nucleocapsid protein (NCp7) for proper viral replication. HIV-1 NCp7 has been shown to enhance various steps in reverse transcription including tRNA initiation and strand transfer, which may be mediated through interactions with RT as well as RNA and DNA oligonucleotides. With the use of DNA oligonucleotides, we have examined the interaction of NCp7 with RT and the kinetics of reverse transcription during (+)-strand synthesis with an NCp7-facilitated annealed primer-template. Through the use of a pre-steady-state kinetics approach, the NCp7-annealed primer-template has a substantial increase (3- to 7-fold) in the rate of incorporation (k(pol)) by RT as compared to heat-annealed primer-template with single-nucleotide incorporation. There was also a 2-fold increase in the binding affinity constant (K(d)) of the nucleotide. These differences in k(pol) and K(d) were not through direct interactions between HIV-1 RT and NCp7. When extension by RT was examined, the data suggest that the NCp7-annealed primer-template facilitates the formation of a longer product more quickly compared to the heat-annealed primer-template. This enhancement in rate is mediated through interactions with NCp7's zinc fingers and N-terminal domain and nucleic acids. The NCp7-annealed primer-template also enhances the fidelity of RT (3-fold) by slowing the rate of incorporation of an incorrect nucleotide. Taken together, this study elucidates a new role of NCp7 by facilitating DNA-directed DNA synthesis during reverse transcription by HIV-1 RT that may translate into enhanced viral fitness and offers an avenue to exploit for targeted therapeutic intervention against HIV.
    Keywords: HIV Reverse Transcriptase -- Metabolism ; Gag Gene Products, Human Immunodeficiency Virus -- Metabolism
    ISSN: 00222836
    E-ISSN: 1089-8638
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