|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
1395 a.a.
|
|
|
|
|
|
|
|
|
|
|
1106 a.a.
|
|
|
|
|
|
|
|
|
|
|
266 a.a.
|
|
|
|
|
|
|
|
|
|
|
214 a.a.
|
|
|
|
|
|
|
|
|
|
|
84 a.a.
|
|
|
|
|
|
|
|
|
|
|
133 a.a.
|
|
|
|
|
|
|
|
|
|
|
119 a.a.
|
|
|
|
|
|
|
|
|
|
|
65 a.a.
|
|
|
|
|
|
|
|
|
|
|
114 a.a.
|
|
|
|
|
|
|
|
|
|
|
46 a.a.
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Transcription/DNA-RNA hybrid
|
|
|
Title:
|
|
RNA polymerase ii strand separated elongation complex
|
|
Structure:
|
|
RNA strand. Chain: r. Engineered: yes. Other_details: transcript. DNA strand. Chain: t. Engineered: yes. Other_details: template. DNA-directed RNA polymerase ii largest subunit.
|
|
Source:
|
|
Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Strain: delta-rpb4
|
|
Biol. unit:
|
|
Dodecamer (from
)
|
|
Resolution:
|
|
|
3.61Å
|
R-factor:
|
0.315
|
R-free:
|
0.343
|
|
|
Authors:
|
|
K.D.Westover,D.A.Bushnell,R.D.Kornberg
|
Key ref:
|
|
K.D.Westover
et al.
(2004).
Structural basis of transcription: separation of RNA from DNA by RNA polymerase II.
Science,
303,
1014-1016.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
20-Feb-04
|
Release date:
|
02-Mar-04
|
|
|
Supersedes:
|
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P04050
(RPB1_YEAST) -
DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
1733 a.a.
1395 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P08518
(RPB2_YEAST) -
DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
1224 a.a.
1106 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P16370
(RPB3_YEAST) -
DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
318 a.a.
266 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P20434
(RPAB1_YEAST) -
DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
215 a.a.
214 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P20435
(RPAB2_YEAST) -
DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
155 a.a.
84 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P20436
(RPAB3_YEAST) -
DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
146 a.a.
133 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P27999
(RPB9_YEAST) -
DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
122 a.a.
119 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P22139
(RPAB5_YEAST) -
DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
70 a.a.
65 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains A, B, C, E, F, H, I, J, K, L:
E.C.2.7.7.6
- DNA-directed Rna polymerase.
|
|
|
|
|
|
|
Reaction:
|
|
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
|
|
|
|
|
|
RNA(n)
|
+
|
ribonucleoside 5'-triphosphate
|
=
|
RNA(n+1)
|
+
|
diphosphate
|
|
|
|
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
Science
303:1014-1016
(2004)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structural basis of transcription: separation of RNA from DNA by RNA polymerase II.
|
|
K.D.Westover,
D.A.Bushnell,
R.D.Kornberg.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The structure of an RNA polymerase II-transcribing complex has been determined
in the posttranslocation state, with a vacancy at the growing end of the RNA-DNA
hybrid helix. At the opposite end of the hybrid helix, the RNA separates from
the template DNA. This separation of nucleic acid strands is brought about by
interaction with a set of proteins loops in a strand/loop network. Formation of
the network must occur in the transition from abortive initiation to promoter
escape.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
Fig. 1. RNA and DNA in the structure of a Pol II-transcribing
complex. (A) Model for RNA and DNA fitted to electron density
for nucleic acids (2F[obs]-F[calc] SigmaA-weighted map, with
phases from Pol II alone, contoured at 0.8 Å). The
direction of viewis from the Rpb2 side of the Pol II structure,
the same as that previously shown of nucleic acids in the
transcribing complex [figure 2C in (1)]. RNA is in magenta and
template DNA is in cyan. A chain-terminating 3'-dA residue is
shown in yellow. (B) Sequences of RNA and DNA in the
transcribing complex. Nucleotide positions are numbered with
respect to the addition site (i+1 site, denoted +1), with
positions upstream extending from -1 and those downstream from
+2. The separation of RNA and DNA strands upstream of -8 is
indicated schematically. (C) Downstream end of the RNA-DNA
hybrid in the previous transcribing-complex structure (1),
showing occupancy of the nucleotide addition (i+1) site. (D)
Downstream end of the RNA-DNA hybrid in the present
transcribing-complex structure, showing vacancy of the
nucleotide-addition site. The "bridge helix" (in green),
extending across the Pol II cleft between the two largest
subunits, and the Mg2+ ion (pink sphere) provide landmarks of
the active-center region and points of reference to previous
structures. Electron density maps (2F[obs]-F[calc]
SigmaA-weighted, with phases from Pol II alone) are shown as
gray nets. Figures were generated by PyMOL (12) or SPOCK (13).
|
|
Figure 2.
Fig. 2. Separation of RNA transcript from DNA template: the
loop/strand network. (A) Portion of Fig. 1A, from residues -2 to
-10, viewed from the front of the transcribing complex (rotated
90° around the RNA-DNA hybrid helix axis in Fig. 1A).
Unpaired bases are colored orange (-8), purple (-9), and gray
(-10). (B) Close-up of residues -7 to -10 of the model in (A).
Average distances (in angstrom) between groups ordinarily
involved in hydrogen bonding between complementary bases are
shown. (C) Electron density for protein loops involved in strand
separation. Backbone models of fork loop 1 (orange), rudder
(green), and lid (purple) are fitted to electron density as in
Fig. 1A. RNA and DNA models are from Fig. 2A. (D) Some residues
of protein loops (carbon atoms, yellow; nitrogen atoms, blue)
interacting with RNA and DNA. Fork loop 1 (Rpb2) residues Lys471
and Arg476, rudder (Rpb1) residues Ser318 and Arg320, and lid
(Rpb1) residue Phe^252 are shown.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from the AAAs:
Science
(2004,
303,
1014-1016)
copyright 2004.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
D.Grohmann,
and
F.Werner
(2010).
Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination.
|
| |
RNA Biol,
7,
310-315.
|
|
|
|
|
|
|
D.Wang,
G.Zhu,
X.Huang,
and
S.J.Lippard
(2010).
X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct.
|
| |
Proc Natl Acad Sci U S A,
107,
9584-9589.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.Grünberg,
C.Reich,
M.E.Zeller,
M.S.Bartlett,
and
M.Thomm
(2010).
Rearrangement of the RNA polymerase subunit H and the lower jaw in archaeal elongation complexes.
|
| |
Nucleic Acids Res,
38,
1950-1963.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
V.Epshtein,
D.Dutta,
J.Wade,
and
E.Nudler
(2010).
An allosteric mechanism of Rho-dependent transcription termination.
|
| |
Nature,
463,
245-249.
|
|
|
|
|
|
|
W.J.Lane,
and
S.A.Darst
(2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
|
| |
J Mol Biol,
395,
686-704.
|
|
|
|
|
|
|
W.J.Lane,
and
S.A.Darst
(2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
|
| |
J Mol Biol,
395,
671-685.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
C.Walmacq,
M.L.Kireeva,
J.Irvin,
Y.Nedialkov,
L.Lubkowska,
F.Malagon,
J.N.Strathern,
and
M.Kashlev
(2009).
Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.
|
| |
J Biol Chem,
284,
19601-19612.
|
|
|
|
|
|
|
C.Y.Chen,
C.C.Chang,
C.F.Yen,
M.T.Chiu,
and
W.H.Chang
(2009).
Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.
|
| |
Proc Natl Acad Sci U S A,
106,
127-132.
|
|
|
|
|
|
|
D.G.Vassylyev
(2009).
Elongation by RNA polymerase: a race through roadblocks.
|
| |
Curr Opin Struct Biol,
19,
691-700.
|
|
|
|
|
|
|
D.Roy,
and
M.R.Lieber
(2009).
G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter.
|
| |
Mol Cell Biol,
29,
3124-3133.
|
|
|
|
|
|
|
D.Wang,
D.A.Bushnell,
X.Huang,
K.D.Westover,
M.Levitt,
and
R.D.Kornberg
(2009).
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
|
| |
Science,
324,
1203-1206.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
J.Andrecka,
B.Treutlein,
M.A.Arcusa,
A.Muschielok,
R.Lewis,
A.C.Cheung,
P.Cramer,
and
J.Michaelis
(2009).
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex.
|
| |
Nucleic Acids Res,
37,
5803-5809.
|
|
|
|
|
|
|
M.L.Kireeva,
and
M.Kashlev
(2009).
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
|
| |
Proc Natl Acad Sci U S A,
106,
8900-8905.
|
|
|
|
|
|
|
P.A.Meyer,
P.Ye,
M.H.Suh,
M.Zhang,
and
J.Fu
(2009).
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
|
| |
J Biol Chem,
284,
12933-12939.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Hahn
(2009).
Structural biology: New beginnings for transcription.
|
| |
Nature,
462,
292-293.
|
|
|
|
|
|
|
T.Kent,
E.Kashkina,
M.Anikin,
and
D.Temiakov
(2009).
Maintenance of RNA-DNA hybrid length in bacterial RNA polymerases.
|
| |
J Biol Chem,
284,
13497-13504.
|
|
|
|
|
|
|
Y.Korkhin,
U.M.Unligil,
O.Littlefield,
P.J.Nelson,
D.I.Stuart,
P.B.Sigler,
S.D.Bell,
and
N.G.Abrescia
(2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
|
| |
PLoS Biol,
7,
e102.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.A.Khaperskyy,
M.L.Ammerman,
R.C.Majovski,
and
A.S.Ponticelli
(2008).
Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization.
|
| |
Mol Cell Biol,
28,
3757-3766.
|
|
|
|
|
|
|
D.Roy,
K.Yu,
and
M.R.Lieber
(2008).
Mechanism of R-loop formation at immunoglobulin class switch sequences.
|
| |
Mol Cell Biol,
28,
50-60.
|
|
|
|
|
|
|
J.Andrecka,
R.Lewis,
F.Brückner,
E.Lehmann,
P.Cramer,
and
J.Michaelis
(2008).
Single-molecule tracking of mRNA exiting from RNA polymerase II.
|
| |
Proc Natl Acad Sci U S A,
105,
135-140.
|
|
|
|
|
|
|
J.L.Huppert
(2008).
Thermodynamic prediction of RNA-DNA duplex-forming regions in the human genome.
|
| |
Mol Biosyst,
4,
686-691.
|
|
|
|
|
|
|
J.N.Kuehner,
and
D.A.Brow
(2008).
Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.
|
| |
Mol Cell,
31,
201-211.
|
|
|
|
|
|
|
L.Zhang,
A.G.Fletcher,
V.Cheung,
F.Winston,
and
L.A.Stargell
(2008).
Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II.
|
| |
Mol Cell Biol,
28,
1393-1403.
|
|
|
|
|
|
|
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,
E.Lehmann,
K.Leike,
J.F.Sydow,
and
A.Vannini
(2008).
Structure of eukaryotic RNA polymerases.
|
| |
Annu Rev Biophys,
37,
337-352.
|
|
|
|
|
|
|
S.M.Soltis,
A.E.Cohen,
A.Deacon,
T.Eriksson,
A.González,
S.McPhillips,
H.Chui,
P.Dunten,
M.Hollenbeck,
I.Mathews,
M.Miller,
P.Moorhead,
R.P.Phizackerley,
C.Smith,
J.Song,
H.van dem Bedem,
P.Ellis,
P.Kuhn,
T.McPhillips,
N.Sauter,
K.Sharp,
I.Tsyba,
and
G.Wolf
(2008).
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
1210-1221.
|
|
|
|
|
|
|
S.Naji,
M.G.Bertero,
P.Spitalny,
P.Cramer,
and
M.Thomm
(2008).
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
|
| |
Nucleic Acids Res,
36,
676-687.
|
|
|
|
|
|
|
S.Nottebaum,
L.Tan,
D.Trzaska,
H.C.Carney,
and
R.O.Weinzierl
(2008).
The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes.
|
| |
Nucleic Acids Res,
36,
245-252.
|
|
|
|
|
|
|
B.P.Somesh,
S.Sigurdsson,
H.Saeki,
H.Erdjument-Bromage,
P.Tempst,
and
J.Q.Svejstrup
(2007).
Communication between distant sites in RNA polymerase II through ubiquitylation factors and the polymerase CTD.
|
| |
Cell,
129,
57-68.
|
|
|
|
|
|
|
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.K.Niu
(2007).
Protecting exons from deleterious R-loops: a potential advantage of having introns.
|
| |
Biol Direct,
2,
11.
|
|
|
|
|
|
|
F.T.Huang,
K.Yu,
B.B.Balter,
E.Selsing,
Z.Oruc,
A.A.Khamlichi,
C.L.Hsieh,
and
M.R.Lieber
(2007).
Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region.
|
| |
Mol Cell Biol,
27,
5921-5932.
|
|
|
|
|
|
|
H.T.Chen,
L.Warfield,
and
S.Hahn
(2007).
The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex.
|
| |
Nat Struct Mol Biol,
14,
696-703.
|
|
|
|
|
|
|
O.I.Kulaeva,
D.A.Gaykalova,
and
V.M.Studitsky
(2007).
Transcription through chromatin by RNA polymerase II: histone displacement and exchange.
|
| |
Mutat Res,
618,
116-129.
|
|
|
|
|
|
|
R.D.Kornberg
(2007).
The molecular basis of eukaryotic transcription.
|
| |
Proc Natl Acad Sci U S A,
104,
12955-12961.
|
|
|
|
|
|
|
R.I.Kraeva,
D.B.Krastev,
A.Roguev,
A.Ivanova,
M.N.Nedelcheva-Veleva,
and
S.S.Stoynov
(2007).
Stability of mRNA/DNA and DNA/DNA duplexes affects mRNA transcription.
|
| |
PLoS ONE,
2,
e290.
|
|
|
|
|
|
|
S.Kaneko,
C.Chu,
A.J.Shatkin,
and
J.L.Manley
(2007).
Human capping enzyme promotes formation of transcriptional R loops in vitro.
|
| |
Proc Natl Acad Sci U S A,
104,
17620-17625.
|
|
|
|
|
|
|
Y.Yamaguchi,
T.Mura,
S.Chanarat,
S.Okamoto,
and
H.Handa
(2007).
Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity.
|
| |
Genes Cells,
12,
863-875.
|
|
|
|
|
|
|
A.J.Jasiak,
K.J.Armache,
B.Martens,
R.P.Jansen,
and
P.Cramer
(2006).
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model.
|
| |
Mol Cell,
23,
71-81.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.M.Deaconescu,
A.L.Chambers,
A.J.Smith,
B.E.Nickels,
A.Hochschild,
N.J.Savery,
and
S.A.Darst
(2006).
Structural basis for bacterial transcription-coupled DNA repair.
|
| |
Cell,
124,
507-520.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.R.Hieb,
S.Baran,
J.A.Goodrich,
and
J.F.Kugel
(2006).
An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation.
|
| |
EMBO J,
25,
3100-3109.
|
|
|
|
|
|
|
A.Saunders,
L.J.Core,
and
J.T.Lis
(2006).
Breaking barriers to transcription elongation.
|
| |
Nat Rev Mol Cell Biol,
7,
557-567.
|
|
|
|
|
|
|
A.Ujvári,
and
D.S.Luse
(2006).
RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit.
|
| |
Nat Struct Mol Biol,
13,
49-54.
|
|
|
|
|
|
|
C.S.Pikaard
(2006).
Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification.
|
| |
Cold Spring Harb Symp Quant Biol,
71,
473-480.
|
|
|
|
|
|
|
F.Malagon,
M.L.Kireeva,
B.K.Shafer,
L.Lubkowska,
M.Kashlev,
and
J.N.Strathern
(2006).
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil.
|
| |
Genetics,
172,
2201-2209.
|
|
|
|
|
|
|
F.T.Huang,
K.Yu,
C.L.Hsieh,
and
M.R.Lieber
(2006).
Downstream boundary of chromosomal R-loops at murine switch regions: implications for the mechanism of class switch recombination.
|
| |
Proc Natl Acad Sci U S A,
103,
5030-5035.
|
|
|
|
|
|
|
G.Miller,
and
S.Hahn
(2006).
A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex.
|
| |
Nat Struct Mol Biol,
13,
603-610.
|
|
|
|
|
|
|
M.Drolet
(2006).
Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology.
|
| |
Mol Microbiol,
59,
723-730.
|
|
|
|
|
|
|
M.Hampsey
(2006).
The Pol II initiation complex: finding a place to start.
|
| |
Nat Struct Mol Biol,
13,
564-566.
|
|
|
|
|
|
|
P.A.Meyer,
P.Ye,
M.Zhang,
M.H.Suh,
and
J.Fu
(2006).
Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.
|
| |
Structure,
14,
973-982.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.D.Auweter,
F.C.Oberstrass,
and
F.H.Allain
(2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
|
| |
Nucleic Acids Res,
34,
4943-4959.
|
|
|
|
|
|
|
T.A.Steitz
(2006).
Visualizing polynucleotide polymerase machines at work.
|
| |
EMBO J,
25,
3458-3468.
|
|
|
|
|
|
|
V.Trinh,
M.F.Langelier,
J.Archambault,
and
B.Coulombe
(2006).
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
|
| |
Microbiol Mol Biol Rev,
70,
12-36.
|
|
|
|
|
|
|
Y.Takagi,
G.Calero,
H.Komori,
J.A.Brown,
A.H.Ehrensberger,
A.Hudmon,
F.Asturias,
and
R.D.Kornberg
(2006).
Head module control of mediator interactions.
|
| |
Mol Cell,
23,
355-364.
|
|
|
|
|
|
|
A.H.Sarker,
S.E.Tsutakawa,
S.Kostek,
C.Ng,
D.S.Shin,
M.Peris,
E.Campeau,
J.A.Tainer,
E.Nogales,
and
P.K.Cooper
(2005).
Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome.
|
| |
Mol Cell,
20,
187-198.
|
|
|
|
|
|
|
B.Coulombe,
and
M.F.Langelier
(2005).
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II.
|
| |
Biochem Cell Biol,
83,
497-504.
|
|
|
|
|
|
|
B.J.Paul,
M.B.Berkmen,
and
R.L.Gourse
(2005).
DksA potentiates direct activation of amino acid promoters by ppGpp.
|
| |
Proc Natl Acad Sci U S A,
102,
7823-7828.
|
|
|
|
|
|
|
J.L.Knight,
V.Mekler,
J.Mukhopadhyay,
R.H.Ebright,
and
R.M.Levy
(2005).
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.
|
| |
Biophys J,
88,
925-938.
|
|
|
|
|
|
|
K.Förstemann,
and
J.Lingner
(2005).
Telomerase limits the extent of base pairing between template RNA and telomeric DNA.
|
| |
EMBO Rep,
6,
361-366.
|
|
|
|
|
|
|
M.A.Freire-Picos,
S.Krishnamurthy,
Z.W.Sun,
and
M.Hampsey
(2005).
Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex.
|
| |
Nucleic Acids Res,
33,
5045-5052.
|
|
|
|
|
|
|
M.F.Langelier,
D.Baali,
V.Trinh,
J.Greenblatt,
J.Archambault,
and
B.Coulombe
(2005).
The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.
|
| |
Nucleic Acids Res,
33,
2629-2639.
|
|
|
|
|
|
|
M.L.Kireeva,
B.Hancock,
G.H.Cremona,
W.Walter,
V.M.Studitsky,
and
M.Kashlev
(2005).
Nature of the nucleosomal barrier to RNA polymerase II.
|
| |
Mol Cell,
18,
97.
|
|
|
|
|
|
|
M.Pal,
A.S.Ponticelli,
and
D.S.Luse
(2005).
The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II.
|
| |
Mol Cell,
19,
101-110.
|
|
|
|
|
|
|
M.Palangat,
D.B.Renner,
D.H.Price,
and
R.Landick
(2005).
A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS.
|
| |
Proc Natl Acad Sci U S A,
102,
15036-15041.
|
|
|
|
|
|
|
S.J.Greive,
and
P.H.von Hippel
(2005).
Thinking quantitatively about transcriptional regulation.
|
| |
Nat Rev Mol Cell Biol,
6,
221-232.
|
|
|
|
|
|
|
S.O.Gudima,
J.Chang,
and
J.M.Taylor
(2005).
Reconstitution in cultured cells of replicating HDV RNA from pairs of less than full-length RNAs.
|
| |
RNA,
11,
90-98.
|
|
|
|
|
|
|
S.Tuske,
S.G.Sarafianos,
X.Wang,
B.Hudson,
E.Sineva,
J.Mukhopadhyay,
J.J.Birktoft,
O.Leroy,
S.Ismail,
A.D.Clark,
C.Dharia,
A.Napoli,
O.Laptenko,
J.Lee,
S.Borukhov,
R.H.Ebright,
and
E.Arnold
(2005).
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
|
| |
Cell,
122,
541-552.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Z.F.Burton,
M.Feig,
X.Q.Gong,
C.Zhang,
Y.A.Nedialkov,
and
Y.Xiong
(2005).
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.
|
| |
Biochem Cell Biol,
83,
486-496.
|
|
|
|
|
|
|
B.S.Chen,
and
M.Hampsey
(2004).
Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation.
|
| |
Mol Cell Biol,
24,
3983-3991.
|
|
|
|
|
|
|
C.Jeronimo,
M.F.Langelier,
M.Zeghouf,
M.Cojocaru,
D.Bergeron,
D.Baali,
D.Forget,
S.Mnaimneh,
A.P.Davierwala,
J.Pootoolal,
M.Chandy,
V.Canadien,
B.K.Beattie,
D.P.Richards,
J.L.Workman,
T.R.Hughes,
J.Greenblatt,
and
B.Coulombe
(2004).
RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits.
|
| |
Mol Cell Biol,
24,
7043-7058.
|
|
|
|
|
|
|
F.J.Asturias
(2004).
Another piece in the transcription initiation puzzle.
|
| |
Nat Struct Mol Biol,
11,
1031-1033.
|
|
|
|
|
|
|
H.Kettenberger,
K.J.Armache,
and
P.Cramer
(2004).
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
|
| |
Mol Cell,
16,
955-965.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.T.Chen,
and
S.Hahn
(2004).
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC.
|
| |
Cell,
119,
169-180.
|
|
|
|
|
|
|
K.D.Westover,
D.A.Bushnell,
and
R.D.Kornberg
(2004).
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
|
| |
Cell,
119,
481-489.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.L.Duquette,
P.Handa,
J.A.Vincent,
A.F.Taylor,
and
N.Maizels
(2004).
Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA.
|
| |
Genes Dev,
18,
1618-1629.
|
|
|
|
|
|
|
S.Hahn
(2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
|
| |
Nat Struct Mol Biol,
11,
394-403.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
| |
Links
