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Structural basis for transcription elongation by bacterial RNA polymerase.
Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. Vassylyev DG, et al. Among authors: perederina a. Nature. 2007 Jul 12;448(7150):157-62. doi: 10.1038/nature05932. Epub 2007 Jun 20. Nature. 2007. PMID: 17581590
The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts …
The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.
Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S. Perederina A, et al. RNA. 2002 Dec;8(12):1548-57. RNA. 2002. PMID: 12515387 Free PMC article.
The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. ...
The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop …
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG. Artsimovitch I, et al. Among authors: perederina a. Cell. 2005 Aug 12;122(3):351-63. doi: 10.1016/j.cell.2005.07.014. Cell. 2005. PMID: 16096056
A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. ...We propose that a rifamycin-induced signal is tra
A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explai
Structural basis of transcription inhibition by antibiotic streptolydigin.
Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Temiakov D, et al. Among authors: perederina a. Mol Cell. 2005 Sep 2;19(5):655-66. doi: 10.1016/j.molcel.2005.07.020. Mol Cell. 2005. PMID: 16167380
Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A
Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus …
Structural basis for transcription inhibition by tagetitoxin.
Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I. Vassylyev DG, et al. Among authors: perederina a. Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. doi: 10.1038/nsmb1015. Epub 2005 Nov 6. Nat Struct Mol Biol. 2005. PMID: 16273103 Free PMC article.
A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from T
A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tg
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.
Symersky J, Perederina A, Vassylyeva MN, Svetlov V, Artsimovitch I, Vassylyev DG. Symersky J, et al. Among authors: perederina a. J Biol Chem. 2006 Jan 20;281(3):1309-12. doi: 10.1074/jbc.C500405200. Epub 2005 Nov 18. J Biol Chem. 2006. PMID: 16298991 Free PMC article.
Gfh1, a GreA homolog from Thermus thermophilus, inhibits rather than activates RNA cleavage. Here we report the structure of the T. thermophilus Gfh1 at 2.4 A resolution revealing a two-domain architecture closely resembling that of GreA. ...We propose that G …
Gfh1, a GreA homolog from Thermus thermophilus, inhibits rather than activates RNA cleavage. Here we report the structure of the T. t …
Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus.
Perederina AA, Vassylyeva MN, Berezin IA, Svetlov V, Artsimovitch I, Vassylyev DG. Perederina AA, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jan 1;62(Pt 1):44-6. doi: 10.1107/S1744309105040297. Epub 2005 Dec 16. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006. PMID: 16511259 Free PMC article.
The GreB and Gfh1 crystals, which were improved by macroseeding, belong to space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters a = b = 148, c = 115.2 A and a = b = 59.3, c = 218.9 A, respectively. Complete diffraction data sets were colle …
The GreB and Gfh1 crystals, which were improved by macroseeding, belong to space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters …
Conformational transition of Sec machinery inferred from bacterial SecYE structures.
Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K, Nureki O. Tsukazaki T, et al. Among authors: perederina a. Nature. 2008 Oct 16;455(7215):988-91. doi: 10.1038/nature07421. Nature. 2008. PMID: 18923527 Free PMC article.
Here we present the 3.2-A-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state of SecYE, in which seve …
Here we present the 3.2-A-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermo …
Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.
Perederina A, Esakova O, Quan C, Khanova E, Krasilnikov AS. Perederina A, et al. EMBO J. 2010 Feb 17;29(4):761-9. doi: 10.1038/emboj.2009.396. Epub 2010 Jan 14. EMBO J. 2010. PMID: 20075859 Free PMC article.
Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. ...Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevi …
Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a cataly …
Substrate recognition by ribonucleoprotein ribonuclease MRP.
Esakova O, Perederina A, Quan C, Berezin I, Krasilnikov AS. Esakova O, et al. Among authors: perederina a. RNA. 2011 Feb;17(2):356-64. doi: 10.1261/rna.2393711. Epub 2010 Dec 20. RNA. 2011. PMID: 21173200 Free PMC article.
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