pH 依赖性构象开关激活转录延伸抑制剂。
pH-dependent conformational switch activates the inhibitor of transcription elongation.
作者信息
Laptenko Oleg, Kim Seung-Sup, Lee Jookyung, Starodubtseva Marina, Cava Fellipe, Berenguer Jose, Kong Xiang-Peng, Borukhov Sergei
机构信息
Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084, USA.
出版信息
EMBO J. 2006 May 17;25(10):2131-41. doi: 10.1038/sj.emboj.7601094. Epub 2006 Apr 20.
Abstract
Gfh1, a transcription factor from Thermus thermophilus, inhibits all catalytic activities of RNA polymerase (RNAP). We characterized the Gfh1 structure, function and possible mechanism of action and regulation. Gfh1 inhibits RNAP by competing with NTPs for coordinating the active site Mg2+ ion. This coordination requires at least two aspartates at the tip of the Gfh1 N-terminal coiled-coil domain (NTD). The overall structure of Gfh1 is similar to that of the Escherichia coli transcript cleavage factor GreA, except for the flipped orientation of the C-terminal domain (CTD). We show that depending on pH, Gfh1-CTD exists in two alternative orientations. At pH above 7, it assumes an inactive 'flipped' orientation seen in the structure, which prevents Gfh1 from binding to RNAP. At lower pH, Gfh1-CTD switches to an active 'Gre-like' orientation, which enables Gfh1 to bind to and inhibit RNAP.
摘要
嗜热栖热菌的转录因子Gfh1可抑制RNA聚合酶（RNAP）的所有催化活性。我们对Gfh1的结构、功能以及可能的作用和调控机制进行了表征。Gfh1通过与NTP竞争以配位活性位点Mg2+离子来抑制RNAP。这种配位需要Gfh1 N端卷曲螺旋结构域（NTD）末端至少两个天冬氨酸。Gfh1的整体结构与大肠杆菌转录切割因子GreA相似，只是C端结构域（CTD）的方向相反。我们发现，根据pH值，Gfh1-CTD存在两种不同的方向。在pH高于7时，它呈现出结构中所见的无活性“翻转”方向，这会阻止Gfh1与RNAP结合。在较低pH值下，Gfh1-CTD会转变为活性“Gre样”方向，使Gfh1能够结合并抑制RNAP。
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本文引用的文献
1
Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage.嗜热水生栖热菌Gfh1的晶体结构，Gfh1是一种Gre因子旁系同源物，它抑制而非刺激转录物切割。
J Mol Biol. 2006 Feb 10;356(1):179-88. doi: 10.1016/j.jmb.2005.10.083. Epub 2005 Nov 17.
2
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.通过RNA聚合酶二级通道进行调控。卷曲螺旋转录因子的结构与功能变异性。
J Biol Chem. 2006 Jan 20;281(3):1309-12. doi: 10.1074/jbc.C500405200. Epub 2005 Nov 18.
3
Bacterial transcription elongation factors: new insights into molecular mechanism of action.细菌转录延伸因子：作用分子机制的新见解
Mol Microbiol. 2005 Mar;55(5):1315-24. doi: 10.1111/j.1365-2958.2004.04481.x.
4
Thinking quantitatively about transcriptional regulation.对转录调控进行定量思考。
Nat Rev Mol Cell Biol. 2005 Mar;6(3):221-32. doi: 10.1038/nrm1588.
5
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.完整的RNA聚合酶II延伸复合物结构及其与NTP和TFIIS的相互作用。
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6
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7
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9
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