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Contents |
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229 a.a.
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1119 a.a.
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1392 a.a.
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95 a.a.
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345 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Transferase
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Title:
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Crystal structure of the RNA polymerase holoenzyme from thermus thermophilus at 2.6a resolution
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Structure:
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RNA polymerase alpha subunit. Chain: a, b, k, l. RNA polymerase beta subunit. Chain: c, m. RNA polymerase beta subunit. Chain: d, n. RNA polymerase omega subunit. Chain: e, o. RNA polymerase sigma-70 subunit.
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Source:
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Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
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Biol. unit:
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Hexamer (from
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Resolution:
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2.60Å
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R-factor:
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0.228
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R-free:
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0.274
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Authors:
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Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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D.G.Vassylyev
et al.
(2002).
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution.
Nature,
417,
712-719.
PubMed id:
DOI:
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Date:
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22-Apr-02
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Release date:
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26-Jun-02
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PROCHECK
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Headers
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References
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Q9Z9H6
(RPOA_THETH) -
DNA-directed RNA polymerase subunit alpha
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Seq:
Struc:
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315 a.a.
229 a.a.
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Q8RQE9
(RPOB_THET8) -
DNA-directed RNA polymerase subunit beta
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Seq:
Struc:
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1119 a.a.
1119 a.a.
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Q8RQE8
(RPOC_THET8) -
DNA-directed RNA polymerase subunit beta'
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Seq:
Struc:
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1524 a.a.
1392 a.a.
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Enzyme class:
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Chains A, B, C, D, E, K, L, M, N, O:
E.C.2.7.7.6
- DNA-directed Rna polymerase.
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Reaction:
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Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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Nucleoside triphosphate
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+
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RNA(n)
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=
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diphosphate
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+
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RNA(n+1)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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RNA polymerase complex
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1 term
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Biological process
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regulation of transcription
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6 terms
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Biochemical function
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transferase activity
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9 terms
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DOI no:
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Nature
417:712-719
(2002)
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PubMed id:
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Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution.
|
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D.G.Vassylyev,
S.Sekine,
O.Laptenko,
J.Lee,
M.N.Vassylyeva,
S.Borukhov,
S.Yokoyama.
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ABSTRACT
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In bacteria, the binding of a single protein, the initiation factor sigma, to a
multi-subunit RNA polymerase core enzyme results in the formation of a
holoenzyme, the active form of RNA polymerase essential for transcription
initiation. Here we report the crystal structure of a bacterial RNA polymerase
holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two
amino-terminal domains of the sigma subunit form a V-shaped structure near the
opening of the upstream DNA-binding channel of the active site cleft. The
carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel,
about 57 A from the N-terminal domains. The extended linker domain forms a
hairpin protruding into the active site cleft, then stretching through the
RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme
structure provides insight into the structural organization of transcription
intermediate complexes and into the mechanism of transcription initiation.
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Selected figure(s)
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Figure 5.
Figure 5: Catalytic centre. a, The Mg2+-binding site. The
slow annealing omit |F[O] - F[C]| map contoured at 4.5  (green)
is shown for Mg2+ ions. Mg2+ ions (magenta) and water molecules
(red) are shown as spheres. b, Superposition of the holoenzyme
(magenta) and Pol II23 (cyan) bridge helices. c, d, Two
conformational states (stereo views) of the bridge helix
(white); in the holoenzyme (c) and in Pol II (d). The G-loop
(purple), modelled for Pol II in d, and the DNA/RNA (cyan/pink)
hybrid^23 (downstream DNA, green), modelled for the holoenzyme
in c, are shown. The catalytic Mg2+ ions are shown as magenta
(c) and cyan (d) spheres.
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Figure 6.
Figure 6: Models of the holoenzyme-nucleic acid complexes.
The protein colour coding is the same as in Fig. 1c, except all
of  '
is shown in white. a, b, The closed (a) and partially melted (b)
promoter complexes. c, d, The same DNA model as in b, but
looking down the dsDNA axis for the holoenzyme (c) and for the
T. aquaticus core (d). The dsDNA (green) contains the -35
(cyan), -10 (red), extended -10 (orange) and +1 to +3 (blue)
promoter regions. A brown dsDNA (b) indicates the downstream
DNA-binding site in the open promoter complex. e, The model of
the holoenzyme complex with the DNA/RNA (blue/green) hybrid and
the ssRNA transcript. The Mg2+ (red) and Pb^2+ (blue) ions are
shown as spheres.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2002,
417,
712-719)
copyright 2002.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
|
|
Reference
|
|
|
|
|
|
F.W.Martinez-Rucobo,
S.Sainsbury,
A.C.Cheung,
and
P.Cramer
(2011).
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
|
| |
EMBO J, 30,
1302-1310.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Heindl,
P.Greenwell,
N.Weingarten,
T.Kiss,
G.Terstyanszky,
and
R.O.Weinzierl
(2011).
Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain.
|
| |
Biochem Soc Trans, 39,
31-35.
|
|
|
|
|
|
|
H.Y.Yeh,
T.C.Chen,
K.M.Liou,
H.T.Hsu,
K.M.Chung,
L.L.Hsu,
and
B.Y.Chang
(2011).
The core-independent promoter-specific interaction of primary sigma factor.
|
| |
Nucleic Acids Res, 39,
913-925.
|
|
|
|
|
|
|
A.Tupin,
M.Gualtieri,
J.P.Leonetti,
and
K.Brodolin
(2010).
The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
|
| |
EMBO J, 29,
2527-2537.
|
|
|
|
|
|
|
D.M.Hinton
(2010).
Transcriptional control in the prereplicative phase of T4 development.
|
| |
Virol J, 7,
289.
|
|
|
|
|
|
|
D.Pupov,
N.Miropolskaya,
A.Sevostyanova,
I.Bass,
I.Artsimovitch,
and
A.Kulbachinskiy
(2010).
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.
|
| |
Nucleic Acids Res, 38,
5784-5796.
|
|
|
|
|
|
|
E.P.Geiduschek,
and
G.A.Kassavetis
(2010).
Transcription of the T4 late genes.
|
| |
Virol J, 7,
288.
|
|
|
|
|
|
|
F.Yu,
J.Shi,
J.Zhou,
J.Gu,
Q.Chen,
J.Li,
W.Cheng,
D.Mao,
L.Tian,
B.B.Buchanan,
L.Li,
L.Chen,
D.Li,
and
S.Luan
(2010).
ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana.
|
| |
Proc Natl Acad Sci U S A, 107,
22332-22337.
|
|
|
|
|
|
|
G.A.Belogurov,
A.Sevostyanova,
V.Svetlov,
and
I.Artsimovitch
(2010).
Functional regions of the N-terminal domain of the antiterminator RfaH.
|
| |
Mol Microbiol, 76,
286-301.
|
|
|
|
|
|
|
G.P.Doherty,
M.J.Fogg,
A.J.Wilkinson,
and
P.J.Lewis
(2010).
Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition.
|
| |
Microbiology, 156,
3532-3543.
|
|
|
|
|
|
|
J.Chen,
S.A.Darst,
and
D.Thirumalai
(2010).
Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
|
| |
Proc Natl Acad Sci U S A, 107,
12523-12528.
|
|
|
|
|
|
|
J.Herrou,
R.Foreman,
A.Fiebig,
and
S.Crosson
(2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
|
| |
Mol Microbiol, 78,
290-304.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Zhang,
M.Palangat,
and
R.Landick
(2010).
Role of the RNA polymerase trigger loop in catalysis and pausing.
|
| |
Nat Struct Mol Biol, 17,
99.
|
|
|
|
|
|
|
K.G.Thakur,
T.Praveena,
and
B.Gopal
(2010).
Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA.
|
| |
J Mol Biol, 397,
1199-1208.
|
|
|
|
|
|
|
L.F.Westblade,
E.A.Campbell,
C.Pukhrambam,
J.C.Padovan,
B.E.Nickels,
V.Lamour,
and
S.A.Darst
(2010).
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
|
| |
Nucleic Acids Res, 38,
8357-8369.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Opalka,
J.Brown,
W.J.Lane,
K.A.Twist,
R.Landick,
F.J.Asturias,
and
S.A.Darst
(2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
|
| |
PLoS Biol, 8,
0.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.G.Devi,
E.A.Campbell,
S.A.Darst,
and
B.E.Nickels
(2010).
Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation.
|
| |
Mol Microbiol, 75,
607-622.
|
|
|
|
|
|
|
R.O.Weinzierl
(2010).
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain.
|
| |
BMC Biol, 8,
134.
|
|
|
|
|
|
|
S.Tagami,
S.Sekine,
T.Kumarevel,
N.Hino,
Y.Murayama,
S.Kamegamori,
M.Yamamoto,
K.Sakamoto,
and
S.Yokoyama
(2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
|
| |
Nature, 468,
978-982.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.J.Gries,
W.S.Kontur,
M.W.Capp,
R.M.Saecker,
and
M.T.Record
(2010).
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex.
|
| |
Proc Natl Acad Sci U S A, 107,
10418-10423.
|
|
|
|
|
|
|
V.Monteil,
A.Kolb,
J.D'Alayer,
P.Beguin,
and
F.Norel
(2010).
Identification of conserved amino acid residues of the Salmonella sigmaS chaperone Crl involved in Crl-sigmaS interactions.
|
| |
J Bacteriol, 192,
1075-1087.
|
|
|
|
|
|
|
W.J.Lane,
and
S.A.Darst
(2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
|
| |
J Mol Biol, 395,
686-704.
|
|
|
|
|
|
|
X.Liu,
D.A.Bushnell,
D.Wang,
G.Calero,
and
R.D.Kornberg
(2010).
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.
|
| |
Science, 327,
206-209.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Yuzenkova,
and
N.Zenkin
(2010).
Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis.
|
| |
Proc Natl Acad Sci U S A, 107,
10878-10883.
|
|
|
|
|
|
|
Z.Baharoglu,
R.Lestini,
S.Duigou,
and
B.Michel
(2010).
RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases.
|
| |
Mol Microbiol, 77,
324-336.
|
|
|
|
|
|
|
A.D.Klocko,
and
K.M.Wassarman
(2009).
6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2.
|
| |
Mol Microbiol, 73,
152-164.
|
|
|
|
|
|
|
A.Rogozina,
E.Zaychikov,
M.Buckle,
H.Heumann,
and
B.Sclavi
(2009).
DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37 degrees C and results in the accumulation of an off-pathway intermediate.
|
| |
Nucleic Acids Res, 37,
5390-5404.
|
|
|
|
|
|
|
A.Tupin,
M.Gualtieri,
K.Brodolin,
and
J.P.Leonetti
(2009).
Myxopyronin: a punch in the jaws of bacterial RNA polymerase.
|
| |
Future Microbiol, 4,
145-149.
|
|
|
|
|
|
|
B.T.Glaser,
V.Bergendahl,
L.C.Anthony,
B.Olson,
and
R.R.Burgess
(2009).
Studying the salt dependence of the binding of sigma70 and sigma32 to core RNA polymerase using luminescence resonance energy transfer.
|
| |
PLoS One, 4,
e6490.
|
|
|
|
|
|
|
C.L.Ross,
K.S.Thomason,
and
T.M.Koehler
(2009).
An extracytoplasmic function sigma factor controls beta-lactamase gene expression in Bacillus anthracis and other Bacillus cereus group species.
|
| |
J Bacteriol, 191,
6683-6693.
|
|
|
|
|
|
|
D.G.Vassylyev
(2009).
Elongation by RNA polymerase: a race through roadblocks.
|
| |
Curr Opin Struct Biol, 19,
691-700.
|
|
|
|
|
|
|
D.Kostrewa,
M.E.Zeller,
K.J.Armache,
M.Seizl,
K.Leike,
M.Thomm,
and
P.Cramer
(2009).
RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
|
| |
Nature, 462,
323-330.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.B.Johnston,
P.J.Lewis,
and
R.Griffith
(2009).
The interaction of Bacillus subtilis sigmaA with RNA polymerase.
|
| |
Protein Sci, 18,
2287-2297.
|
|
|
|
|
|
|
E.Nudler
(2009).
RNA polymerase active center: the molecular engine of transcription.
|
| |
Annu Rev Biochem, 78,
335-361.
|
|
|
|
|
|
|
F.Brueckner,
J.Ortiz,
and
P.Cramer
(2009).
A movie of the RNA polymerase nucleotide addition cycle.
|
| |
Curr Opin Struct Biol, 19,
294-299.
|
|
|
|
|
|
|
F.Brueckner,
K.J.Armache,
A.Cheung,
G.E.Damsma,
H.Kettenberger,
E.Lehmann,
J.Sydow,
and
P.Cramer
(2009).
Structure-function studies of the RNA polymerase II elongation complex.
|
| |
Acta Crystallogr D Biol Crystallogr, 65,
112-120.
|
|
|
|
|
|
|
G.A.Belogurov,
M.N.Vassylyeva,
A.Sevostyanova,
J.R.Appleman,
A.X.Xiang,
R.Lira,
S.E.Webber,
S.Klyuyev,
E.Nudler,
I.Artsimovitch,
and
D.G.Vassylyev
(2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
|
| |
Nature, 457,
332-335.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Spåhr,
G.Calero,
D.A.Bushnell,
and
R.D.Kornberg
(2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
|
| |
Proc Natl Acad Sci U S A, 106,
9185-9190.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.G.Hook-Barnard,
and
D.M.Hinton
(2009).
The promoter spacer influences transcription initiation via {sigma}70 region 1.1 of Escherichia coli RNA polymerase.
|
| |
Proc Natl Acad Sci U S A, 106,
737-742.
|
|
|
|
|
|
|
K.B.Decker,
and
D.M.Hinton
(2009).
The secret to 6S: regulating RNA polymerase by ribo-sequestration.
|
| |
Mol Microbiol, 73,
137-140.
|
|
|
|
|
|
|
L.A.Schroeder,
T.J.Gries,
R.M.Saecker,
M.T.Record,
M.E.Harris,
and
P.L.DeHaseth
(2009).
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.
|
| |
J Mol Biol, 385,
339-349.
|
|
|
|
|
|
|
M.X.Ho,
B.P.Hudson,
K.Das,
E.Arnold,
and
R.H.Ebright
(2009).
Structures of RNA polymerase-antibiotic complexes.
|
| |
Curr Opin Struct Biol, 19,
715-723.
|
|
|
|
|
|
|
N.E.Thompson,
B.T.Glaser,
K.M.Foley,
Z.F.Burton,
and
R.R.Burgess
(2009).
Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB.
|
| |
J Biol Chem, 284,
24754-24766.
|
|
|
|
|
|
|
N.Miropolskaya,
I.Artsimovitch,
S.Klimasauskas,
V.Nikiforov,
and
A.Kulbachinskiy
(2009).
Allosteric control of catalysis by the F loop of RNA polymerase.
|
| |
Proc Natl Acad Sci U S A, 106,
18942-18947.
|
|
|
|
|
|
|
S.Hahn
(2009).
Structural biology: New beginnings for transcription.
|
| |
Nature, 462,
292-293.
|
|
|
|
|
|
|
S.Imamura,
and
M.Asayama
(2009).
Sigma factors for cyanobacterial transcription.
|
| |
Gene Regul Syst Bio, 3,
65-87.
|
|
|
|
|
|
|
S.T.Rutherford,
C.L.Villers,
J.H.Lee,
W.Ross,
and
R.L.Gourse
(2009).
Allosteric control of Escherichia coli rRNA promoter complexes by DksA.
|
| |
Genes Dev, 23,
236-248.
|
|
|
|
|
|
|
X.Rao,
P.Deighan,
Z.Hua,
X.Hu,
J.Wang,
M.Luo,
J.Wang,
Y.Liang,
G.Zhong,
A.Hochschild,
and
L.Shen
(2009).
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Genes Dev, 23,
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Y.Korkhin,
U.M.Unligil,
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Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
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PLoS Biol, 7,
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PDB codes:
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|
A.Casañas,
A.Navarro,
C.Ferrer-Orta,
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J.F.Rodríguez,
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Structural insights into the multifunctional protein VP3 of birnaviruses.
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Structure, 16,
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PDB codes:
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A.H.Yuan,
B.D.Gregory,
J.S.Sharp,
K.D.McCleary,
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Mol Microbiol, 70,
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A.Sevostyanova,
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Proc Natl Acad Sci U S A, 105,
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Biochim Biophys Acta, 1778,
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C.D.Kaplan,
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The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
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Mol Cell, 30,
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PDB code:
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C.D.Kaplan,
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A bridge to transcription by RNA polymerase.
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J Biol, 7,
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C.E.Vrentas,
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Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
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J Mol Biol, 377,
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D.Bose,
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S.R.Wigneshweraraj,
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Mol Cell, 32,
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E.A.Campbell,
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Curr Opin Microbiol, 11,
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A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding.
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Chem Biol, 15,
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PDB code:
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|
|
F.Brueckner,
and
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Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
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Nat Struct Mol Biol, 15,
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PDB code:
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|
|
|
|
|
|
F.Cava,
M.A.de Pedro,
E.Blas-Galindo,
G.S.Waldo,
L.F.Westblade,
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Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology.
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Environ Microbiol, 10,
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F.Rodriguez,
F.Arsène-Ploetze,
W.Rist,
S.Rüdiger,
J.Schneider-Mergener,
M.P.Mayer,
and
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Molecular basis for regulation of the heat shock transcription factor sigma32 by the DnaK and DnaJ chaperones.
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Mol Cell, 32,
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J.Mukhopadhyay,
K.Das,
S.Ismail,
D.Koppstein,
M.Jang,
B.Hudson,
S.Sarafianos,
S.Tuske,
J.Patel,
R.Jansen,
H.Irschik,
E.Arnold,
and
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The RNA polymerase "switch region" is a target for inhibitors.
|
| |
Cell, 135,
295-307.
|
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PDB code:
|
|
|
|
|
|
|
|
K.J.Durniak,
S.Bailey,
and
T.A.Steitz
(2008).
The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation.
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| |
Science, 322,
553-557.
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|
PDB codes:
|
|
|
|
|
|
|
|
L.Tan,
S.Wiesler,
D.Trzaska,
H.C.Carney,
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Bridge helix and trigger loop perturbations generate superactive RNA polymerases.
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J Biol, 7,
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M.Dekhtyar,
A.Morin,
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Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes.
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BMC Bioinformatics, 9,
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M.Djordjevic,
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Formation of the open complex by bacterial RNA polymerase--a quantitative model.
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Biophys J, 94,
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B.L.Suresh,
A.Goh,
J.E.Knox,
N.L.Ma,
J.Jiricek,
D.Beer,
M.Cynamon,
F.Petersen,
V.Dartois,
T.Keller,
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Lipiarmycin targets RNA polymerase and has good activity against multidrug-resistant strains of Mycobacterium tuberculosis.
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J Antimicrob Chemother, 62,
713-719.
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N.Barinova,
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Lineage-specific amino acid substitutions in region 2 of the RNA polymerase sigma subunit affect the temperature of promoter opening.
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| |
J Bacteriol, 190,
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N.Barinova,
K.Kuznedelov,
K.Severinov,
and
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Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
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| |
J Biol Chem, 283,
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P.Cramer,
K.J.Armache,
S.Baumli,
S.Benkert,
F.Brueckner,
C.Buchen,
G.E.Damsma,
S.Dengl,
S.R.Geiger,
A.J.Jasiak,
A.Jawhari,
S.Jennebach,
T.Kamenski,
H.Kettenberger,
C.D.Kuhn,
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K.Leike,
J.F.Sydow,
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Structure of eukaryotic RNA polymerases.
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Annu Rev Biophys, 37,
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The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase.
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| |
Proc Natl Acad Sci U S A, 105,
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P.England,
L.F.Westblade,
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Binding of the unorthodox transcription activator, crl, to the components of the transcription machinery.
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J Biol Chem, 283,
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R.P.Bonocora,
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M.H.Werner,
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A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription.
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| |
Mol Microbiol, 69,
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S.Borukhov,
and
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RNA polymerase: the vehicle of transcription.
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Trends Microbiol, 16,
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S.Naji,
M.G.Bertero,
P.Spitalny,
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Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
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| |
Nucleic Acids Res, 36,
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|
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S.Nottebaum,
L.Tan,
D.Trzaska,
H.C.Carney,
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The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes.
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| |
Nucleic Acids Res, 36,
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S.P.Haugen,
W.Ross,
M.Manrique,
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Fine structure of the promoter-sigma region 1.2 interaction.
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| |
Proc Natl Acad Sci U S A, 105,
3292-3297.
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S.P.Haugen,
W.Ross,
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(2008).
Advances in bacterial promoter recognition and its control by factors that do not bind DNA.
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| |
Nat Rev Microbiol, 6,
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S.Wigneshweraraj,
D.Bose,
P.C.Burrows,
N.Joly,
J.Schumacher,
M.Rappas,
T.Pape,
X.Zhang,
P.Stockley,
K.Severinov,
and
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Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor.
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| |
Mol Microbiol, 68,
538-546.
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|
V.Svetlov,
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Jamming the ratchet of transcription.
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| |
Nat Struct Mol Biol, 15,
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Y.Tutar
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Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
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| |
Protein J, 27,
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A.Sevostyanova,
A.Feklistov,
N.Barinova,
E.Heyduk,
I.Bass,
S.Klimasauskas,
T.Heyduk,
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(2007).
Specific recognition of the -10 promoter element by the free RNA polymerase sigma subunit.
|
| |
J Biol Chem, 282,
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A.Shinkai,
N.Ohbayashi,
T.Terada,
M.Shirouzu,
S.Kuramitsu,
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Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8.
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| |
J Bacteriol, 189,
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A.Shinkai,
S.Kira,
N.Nakagawa,
A.Kashihara,
S.Kuramitsu,
and
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(2007).
Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8.
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| |
J Bacteriol, 189,
3891-3901.
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|
A.Szalewska-Palasz,
L.U.Johansson,
L.M.Bernardo,
E.Skärfstad,
E.Stec,
K.Brännström,
and
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(2007).
Properties of RNA polymerase bypass mutants: implications for the role of ppGpp and its co-factor DksA in controlling transcription dependent on sigma54.
|
| |
J Biol Chem, 282,
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|
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A.Typas,
G.Becker,
and
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(2007).
The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.
|
| |
Mol Microbiol, 63,
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|
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|
|
B.T.Glaser,
V.Bergendahl,
N.E.Thompson,
B.Olson,
and
R.R.Burgess
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LRET-based HTS of a small-compound library for inhibitors of bacterial RNA polymerase.
|
| |
Assay Drug Dev Technol, 5,
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|
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|
|
C.A.Davis,
C.A.Bingman,
R.Landick,
M.T.Record,
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Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase.
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| |
Proc Natl Acad Sci U S A, 104,
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C.Zaros,
J.F.Briand,
Y.Boulard,
S.Labarre-Mariotte,
M.C.Garcia-Lopez,
P.Thuriaux,
and
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Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
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| |
Nucleic Acids Res, 35,
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D.G.Vassylyev,
M.N.Vassylyeva,
A.Perederina,
T.H.Tahirov,
and
I.Artsimovitch
(2007).
Structural basis for transcription elongation by bacterial RNA polymerase.
|
| |
Nature, 448,
157-162.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.G.Vassylyev,
M.N.Vassylyeva,
J.Zhang,
M.Palangat,
I.Artsimovitch,
and
R.Landick
(2007).
Structural basis for substrate loading in bacterial RNA polymerase.
|
| |
Nature, 448,
163-168.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.Vingadassalom,
A.Kolb,
C.Mayer,
E.Collatz,
and
I.Podglajen
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Probing the importance of selected phylum-specific amino acids in sigma A of Bacteroides fragilis, a primary sigma factor naturally devoid of an N-terminal acidic region 1.1.
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| |
J Biol Chem, 282,
3442-3449.
|
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E.A.Campbell,
R.Greenwell,
J.R.Anthony,
S.Wang,
L.Lim,
K.Das,
H.J.Sofia,
T.J.Donohue,
and
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(2007).
A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria.
|
| |
Mol Cell, 27,
793-805.
|
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PDB codes:
|
|
|
|
|
|
|
|
E.A.Lysenko
(2007).
Plant sigma factors and their role in plastid transcription.
|
| |
Plant Cell Rep, 26,
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E.Blas-Galindo,
F.Cava,
E.López-Viñas,
J.Mendieta,
and
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Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus.
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| |
Appl Environ Microbiol, 73,
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G.A.Belogurov,
M.N.Vassylyeva,
V.Svetlov,
S.Klyuyev,
N.V.Grishin,
D.G.Vassylyev,
and
I.Artsimovitch
(2007).
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
|
| |
Mol Cell, 26,
117-129.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.A.Patikoglou,
L.F.Westblade,
E.A.Campbell,
V.Lamour,
W.J.Lane,
and
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(2007).
Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.
|
| |
J Mol Biol, 372,
649-659.
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PDB code:
|
|
|
|
|
|
|
|
I.Toulokhonov,
J.Zhang,
M.Palangat,
and
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(2007).
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.
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| |
Mol Cell, 27,
406-419.
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J.Luo,
and
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A multistep process gave rise to RNA polymerase IV of land plants.
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J Mol Evol, 64,
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L.A.Schroeder,
A.J.Choi,
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The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact.
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| |
Nucleic Acids Res, 35,
4141-4153.
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M.Doucleff,
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P.S.Lee,
B.T.Nixon,
and
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(2007).
Structural basis of DNA recognition by the alternative sigma-factor, sigma54.
|
| |
J Mol Biol, 369,
1070-1078.
|
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PDB codes:
|
|
|
|
|
|
|
|
M.Leibman,
and
A.Hochschild
(2007).
A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape.
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| |
EMBO J, 26,
1579-1590.
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M.N.Vassylyeva,
V.Svetlov,
A.D.Dearborn,
S.Klyuyev,
I.Artsimovitch,
and
D.G.Vassylyev
(2007).
The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors.
|
| |
EMBO Rep, 8,
1038-1043.
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PDB code:
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|
|
|
|
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|
N.Zenkin,
A.Kulbachinskiy,
Y.Yuzenkova,
A.Mustaev,
I.Bass,
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Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element.
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EMBO J, 26,
955-964.
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P.Sadhale,
J.Verma,
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Basal transcription machinery: role in regulation of stress response in eukaryotes.
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J Biosci, 32,
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Q.Wang,
T.D.Tullius,
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Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase.
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J Biol Chem, 282,
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R.K.Shultzaberger,
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K.A.Lewis,
and
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Anatomy of Escherichia coli sigma70 promoters.
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Nucleic Acids Res, 35,
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T.J.Santangelo,
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TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro.
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J Mol Biol, 367,
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V.Epshtein,
C.J.Cardinale,
A.E.Ruckenstein,
S.Borukhov,
and
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An allosteric path to transcription termination.
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| |
Mol Cell, 28,
991.
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V.Svetlov,
G.A.Belogurov,
E.Shabrova,
D.G.Vassylyev,
and
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Allosteric control of the RNA polymerase by the elongation factor RfaH.
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Nucleic Acids Res, 35,
5694-5705.
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Y.A.Khodak,
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A system for heterologous expression and isolation of Escherichia coli RNA polymerase and its components.
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Biochemistry (Mosc), 72,
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Y.Devedjiev,
C.N.Steussy,
and
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(2007).
Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications.
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| |
J Mol Biol, 370,
407-416.
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PDB code:
|
|
|
|
|
|
|
|
A.Feklistov,
N.Barinova,
A.Sevostyanova,
E.Heyduk,
I.Bass,
I.Vvedenskaya,
K.Kuznedelov,
E.Merkiene,
E.Stavrovskaya,
S.Klimasauskas,
V.Nikiforov,
T.Heyduk,
K.Severinov,
and
A.Kulbachinskiy
(2006).
A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.
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| |
Mol Cell, 23,
97.
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|
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A.Kulbachinskiy,
and
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