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Contents |
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224 a.a.
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1084 a.a.
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1183 a.a.
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92 a.a.
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322 a.a.
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* Residue conservation analysis
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PDB id:
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Transcription
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Title:
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Thermus aquaticus RNA polymerase holoenzyme at 4 a resolution
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Structure:
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RNA polymerase, alpha subunit. Chain: a, b, j, k. RNA polymerase, beta subunit. Chain: c, l. RNA polymerase, beta-prime subunit. Chain: d, m. RNA polymerase, omega subunit. Chain: e, n. Sigma factor siga.
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Source:
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Thermus aquaticus. Organism_taxid: 271. Gene: rpod. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Hexamer (from
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Resolution:
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4.00Å
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R-factor:
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not given
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Authors:
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K.S.Murakami,S.Masuda,S.A.Darst
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Key ref:
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K.S.Murakami
et al.
(2002).
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
Science,
296,
1280-1284.
PubMed id:
DOI:
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Date:
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26-Mar-02
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Release date:
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22-May-02
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PROCHECK
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Headers
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References
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Q9KWU8
(RPOA_THEAQ) -
DNA-directed RNA polymerase subunit alpha
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Seq:
Struc:
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314 a.a.
224 a.a.
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Q9KWU7
(RPOB_THEAQ) -
DNA-directed RNA polymerase subunit beta
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Seq:
Struc:
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1119 a.a.
1084 a.a.
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Q9KWU6
(RPOC_THEAQ) -
DNA-directed RNA polymerase subunit beta'
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Seq:
Struc:
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1524 a.a.
1183 a.a.
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Enzyme class:
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Chains A, B, C, D, E, J, K, L, M, N:
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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DNA repair
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5 terms
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Biochemical function
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transferase activity
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8 terms
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DOI no:
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Science
296:1280-1284
(2002)
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PubMed id:
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Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
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K.S.Murakami,
S.Masuda,
S.A.Darst.
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ABSTRACT
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The crystal structure of the initiating form of Thermus aquaticus RNA
polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the
promoter specificity sigma subunit, has been determined at 4 angstrom
resolution. Important structural features of the RNA polymerase and their roles
in positioning sigma within the initiation complex are delineated, as well as
the role played by sigma in modulating the opening of the RNA polymerase
active-site channel. The two carboxyl-terminal domains of sigma are separated by
45 angstroms on the surface of the RNA polymerase, but are linked by an extended
loop. The loop winds near the RNA polymerase active site, where it may play a
role in initiating nucleotide substrate binding, and out through the RNA exit
channel. The advancing RNA transcript must displace the loop, leading to
abortive initiation and ultimately to sigma release.
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Selected figure(s)
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Figure 2.
Fig. 2. Taq RNAP holoenzyme structure. Views of the Taq RNAP
holoenzyme structure, shown as a molecular surface but with
important features of core RNAP shown as  -carbon
backbone worms without the corresponding surfaces (color coding
of surfaces and worms is indicated). The molecular surface of
 is
transparent, allowing the orange -carbon
backbone worm to be seen as well. (A) The same view as in Fig.
1A. The Zn2+ ion bound in the  'ZBD is
shown as a light-green sphere. Surfaces of
corresponding to residues important for promoter recognition and
melting are color coded as follows: melting/  10 element
nontemplate strand binding, yellow; 10 element
recognition, green; extended 10 element
recognition, blue; 35 element
recognition, brown. (B) Partial, magnified view, obtained from
(A) by rotation about the horizontal axis as indicated.
Obscuring portions of have been
removed to reveal the inside of the main channel. The outline of
is shown
as a cyan line. The active-site Mg2+ is shown as a magenta
sphere. The disordered segment of is
denoted by orange dots, connecting residues
336 to 346, which are labeled. The NH[2]-terminus of the fragment
(corresponding to Taq A residue
93), which points into the RNAP channel toward the active-site
Mg2+, is indicated (N). The figure was made with the program
GRASP (41).
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Figure 4.
Fig. 4. Electrostatic distribution of holoenzyme and region
1.1. (A) Two surface views of the RNAP holoenzyme, color coded
according to electrostatic surface potential (negative, red;
neutral, white; positive, blue). The transparent -carbon
backbone worm of (orange)
is superimposed. (Left) Same view as in Fig. 1A. (Right) View
obtained from the left view by a rotation about the vertical
axis as indicated; the active-site Mg2+ in the back of the main
RNAP channel is visible as a magenta sphere. The NH[2]-terminus
of the fragment
(corresponding to Taq A residue
93), which points into the RNAP channel toward the active-site
Mg2+, is indicated (N). (B) Schematic diagram illustrating the
proposed mechanism of the negatively charged region
1.1 in promoting open complex formation. The viewing angle is
similar to that in Fig. 1A. Two states of the RNAP
holoenzyme-promoter DNA complex are illustrated. The positioning
of the DNA is according to (35). The core RNAP is colored gray,
and is
colored orange, except region 1.1, which is colored magenta.
(Left) The initial closed promoter complex (RP[c]), where we
propose that region
1.1 is positioned inside the positively charged RNAP channel
[protecting it from hydroxyl-radical cleavage (34)], holding the
channel open (indicated by thick black lines) to allow entry of
double-stranded DNA. (Right) Final open promoter complex
(RP[o]), where DNA has entered the RNAP main channel and the
channel has closed, ejecting region
1.1, where it is exposed in solution to proteases (35) and
hydroxyl-radical cleavage (34). (A) was made with the program
GRASP (41).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
296,
1280-1284)
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
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Reference
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|
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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.
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| |
EMBO J, 30,
1302-1310.
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PDB code:
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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.
|
|
|
|
|
|
|
J.Trepreau,
E.Girard,
A.P.Maillard,
E.de Rosny,
I.Petit-Haertlein,
R.Kahn,
and
J.Covès
(2011).
Structural Basis for Metal Sensing by CnrX.
|
| |
J Mol Biol, 408,
766-779.
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PDB codes:
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S.H.Jun,
M.J.Reichlen,
M.Tajiri,
and
K.S.Murakami
(2011).
Archaeal RNA polymerase and transcription regulation.
|
| |
Crit Rev Biochem Mol Biol, 46,
27-40.
|
|
|
|
|
|
|
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.
|
|
|
|
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|
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B.Cámara,
M.Liu,
J.Reynolds,
A.Shadrin,
B.Liu,
K.Kwok,
P.Simpson,
R.Weinzierl,
K.Severinov,
E.Cota,
S.Matthews,
and
S.R.Wigneshweraraj
(2010).
T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site.
|
| |
Proc Natl Acad Sci U S A, 107,
2247-2252.
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PDB code:
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D.M.Hinton
(2010).
Transcriptional control in the prereplicative phase of T4 development.
|
| |
Virol J, 7,
289.
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|
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|
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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.
|
|
|
|
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|
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E.P.Geiduschek,
and
G.A.Kassavetis
(2010).
Transcription of the T4 late genes.
|
| |
Virol J, 7,
288.
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|
|
|
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|
|
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.
|
|
|
|
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|
|
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.
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|
|
PDB code:
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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.
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|
PDB code:
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|
|
|
|
|
|
M.K.Taha,
S.T.Hedberg,
M.Szatanik,
E.Hong,
C.Ruckly,
R.Abad,
S.Bertrand,
F.Carion,
H.Claus,
A.Corso,
R.Enríquez,
S.Heuberger,
W.Hryniewicz,
K.A.Jolley,
P.Kriz,
M.Mollerach,
M.Musilek,
A.Neri,
P.Olcén,
M.Pana,
A.Skoczynska,
C.Sorhouet Pereira,
P.Stefanelli,
G.Tzanakaki,
M.Unemo,
J.A.Vázquez,
U.Vogel,
and
I.Wasko
(2010).
Multicenter study for defining the breakpoint for rifampin resistance in Neisseria meningitidis by rpoB sequencing.
|
| |
Antimicrob Agents Chemother, 54,
3651-3658.
|
|
|
|
|
|
|
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.
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|
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PDB codes:
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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.
|
|
|
|
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|
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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.
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|
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PDB codes:
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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.
|
|
|
|
|
|
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W.J.Lane,
and
S.A.Darst
(2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
|
| |
J Mol Biol, 395,
686-704.
|
|
|
|
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|
|
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.
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PDB code:
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|
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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.
|
|
|
|
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|
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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.Hirata,
and
K.S.Murakami
(2009).
Archaeal RNA polymerase.
|
| |
Curr Opin Struct Biol, 19,
724-731.
|
|
|
|
|
|
|
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.
|
|
|
|
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|
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B.M.Koo,
V.A.Rhodius,
E.A.Campbell,
and
C.A.Gross
(2009).
Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element.
|
| |
Mol Microbiol, 72,
830-843.
|
|
|
|
|
|
|
B.M.Koo,
V.A.Rhodius,
E.A.Campbell,
and
C.A.Gross
(2009).
Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element.
|
| |
Mol Microbiol, 72,
815-829.
|
|
|
|
|
|
|
C.L.Stallings,
N.C.Stephanou,
L.Chu,
A.Hochschild,
B.E.Nickels,
and
M.S.Glickman
(2009).
CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence.
|
| |
Cell, 138,
146-159.
|
|
|
|
|
|
|
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:
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|
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|
|
E.B.Johnston,
P.J.Lewis,
and
R.Griffith
(2009).
The interaction of Bacillus subtilis sigmaA with RNA polymerase.
|
| |
Protein Sci, 18,
2287-2297.
|
|
|
|
|
|
|
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:
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|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.R.Gassman,
S.O.Ho,
Y.Korlann,
J.Chiang,
Y.Wu,
L.J.Perry,
Y.Kim,
and
S.Weiss
(2009).
In vivo assembly and single-molecule characterization of the transcription machinery from Shewanella oneidensis MR-1.
|
| |
Protein Expr Purif, 65,
66-76.
|
|
|
|
|
|
|
P.Yan,
T.Wang,
G.J.Newton,
T.V.Knyushko,
Y.Xiong,
D.J.Bigelow,
T.C.Squier,
and
M.U.Mayer
(2009).
A targeted releasable affinity probe (TRAP) for in vivo photocrosslinking.
|
| |
Chembiochem, 10,
1507-1518.
|
|
|
|
|
|
|
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.Kühner,
V.van Noort,
M.J.Betts,
A.Leo-Macias,
C.Batisse,
M.Rode,
T.Yamada,
T.Maier,
S.Bader,
P.Beltran-Alvarez,
D.Castaño-Diez,
W.H.Chen,
D.Devos,
M.Güell,
T.Norambuena,
I.Racke,
V.Rybin,
A.Schmidt,
E.Yus,
R.Aebersold,
R.Herrmann,
B.Böttcher,
A.S.Frangakis,
R.B.Russell,
L.Serrano,
P.Bork,
and
A.C.Gavin
(2009).
Proteome organization in a genome-reduced bacterium.
|
| |
Science, 326,
1235-1240.
|
|
|
|
|
|
|
S.M.Cheal,
M.Ng,
B.Barrios,
Z.Miao,
A.K.Kalani,
and
C.F.Meares
(2009).
Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radical.
|
| |
Biochemistry, 48,
4577-4586.
|
|
|
|
|
|
|
A.H.Yuan,
B.D.Gregory,
J.S.Sharp,
K.D.McCleary,
S.L.Dove,
and
A.Hochschild
(2008).
Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor.
|
| |
Mol Microbiol, 70,
1136-1151.
|
|
|
|
|
|
|
A.Hatoum,
and
J.Roberts
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C.E.Vrentas,
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PDB codes:
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PDB code:
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PDB codes:
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Nat Struct Mol Biol, 11,
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Conserved region 2.1 of Escherichia coli heat shock transcription factor sigma32 is required for modulating both metabolic stability and transcriptional activity.
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Proc Natl Acad Sci U S A, 101,
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Structure and mechanism of the RNA polymerase II transcription machinery.
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Asynchronous basepair openings in transcription initiation: CRP enhances the rate-limiting step.
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EMBO J, 23,
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Autonomous function of the amino-terminal inhibitory domain of TAF1 in transcriptional regulation.
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W.V.Cannon,
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Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein.
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Nucleic Acids Res, 32,
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A.Stüdemann,
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Proc Natl Acad Sci U S A, 100,
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PDB code:
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D.H.Wells,
and
S.R.Long
(2003).
Mutations in rpoBC suppress the defects of a Sinorhizobium meliloti relA mutant.
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J Bacteriol, 185,
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RNA polymerase II at initiation.
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Architecture of initiation-competent 12-subunit RNA polymerase II.
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Proc Natl Acad Sci U S A, 100,
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PDB code:
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|
|
K.S.Murakami,
and
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Bacterial RNA polymerases: the wholo story.
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Structural biology: a high-tech tool for biomedical research.
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The sigma70 family of sigma factors.
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Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
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Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III.
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The FecI extracytoplasmic-function sigma factor of Escherichia coli interacts with the beta' subunit of RNA polymerase.
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|
PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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|
| |
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