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PDBsum entry 2ppb
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Transferase/DNA/RNA
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PDB id
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2ppb
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Contents |
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229 a.a.
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1119 a.a.
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1314 a.a.
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95 a.a.
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References listed in PDB file
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Key reference
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Title
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Structural basis for substrate loading in bacterial RNA polymerase.
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Authors
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D.G.Vassylyev,
M.N.Vassylyeva,
J.Zhang,
M.Palangat,
I.Artsimovitch,
R.Landick.
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Ref.
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Nature, 2007,
448,
163-168.
[DOI no: ]
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PubMed id
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Abstract
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The mechanism of substrate loading in multisubunit RNA polymerase is crucial for
understanding the general principles of transcription yet remains hotly debated.
Here we report the 3.0-A resolution structures of the Thermus thermophilus
elongation complex (EC) with a non-hydrolysable substrate analogue,
adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP
plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate
binds to the active ('insertion') site closed through refolding of the trigger
loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin
structure reveals an inactive ('preinsertion') substrate configuration
stabilized by streptolydigin-induced displacement of the TL. Our structural and
biochemical data suggest that refolding of the TL is vital for catalysis and
have three main implications. First, despite differences in the details, the
two-step preinsertion/insertion mechanism of substrate loading may be universal
for all RNA polymerases. Second, freezing of the preinsertion state is an
attractive target for the design of novel antibiotics. Last, the TL emerges as a
prominent target whose refolding can be modulated by regulatory factors.
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Figure 1.
Figure 1: Structures of the substrate complexes. The same
colour scheme is used in all figures. The DNA template,
non-template and RNA strands are in red, blue and yellow,
respectively. The BH, the TH and the rest of the RNAP molecule
are in magenta, cyan and grey, respectively. The insertion and
preinsertion NTP analogues and Stl are designated by green,
orange and black, respectively. The catalytic Mg^2+ ions (MgI
and MgII) are shown as magenta spheres. a, b, Overall views of
the ttEC/AMPcPP (a) and EC/AMPcPP/Stl (b) complexes. CC, coiled
coil. c, d, Superposition of the NTPs (c, d) and TH (d) in the
insertion (green, NTP; cyan, TH) and preinsertion (orange, NTP;
blue, TH) complexes.
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Figure 5.
Figure 5: Nucleotide addition cycle. The substrate loading
pathway in bacterial RNAP.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
448,
163-168)
copyright 2007.
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