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PDBsum entry 2bf0
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Transcription
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PDB id
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2bf0
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Contents |
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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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Crystal structure of the rpr of pcf11
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Structure:
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Pcf11. Chain: x. Fragment: cid, residues 1-138. Engineered: yes
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Source:
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Saccharomyces cerevisiae. Bakers yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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2.30Å
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R-factor:
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0.260
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R-free:
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0.282
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Authors:
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C.G.Noble,D.Hollingworth,S.R.Martin,V.E.Adeniran,S.J.Smerdon,G.Kelly, I.A.Taylor,A.Ramos
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Key ref:
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C.G.Noble
et al.
(2005).
Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
Nat Struct Mol Biol,
12,
144-151.
PubMed id:
DOI:
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Date:
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02-Dec-04
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Release date:
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18-Jan-05
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PROCHECK
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Headers
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References
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P39081
(PCF11_YEAST) -
Protein PCF11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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626 a.a.
131 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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DOI no:
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Nat Struct Mol Biol
12:144-151
(2005)
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PubMed id:
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Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
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C.G.Noble,
D.Hollingworth,
S.R.Martin,
V.Ennis-Adeniran,
S.J.Smerdon,
G.Kelly,
I.A.Taylor,
A.Ramos.
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ABSTRACT
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The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a
platform for mRNA processing factors and links gene transcription to mRNA
capping, splicing and polyadenylation. Pcf11, an essential component of the mRNA
cleavage factor IA, contains a CTD-interaction domain that binds in a
phospho-dependent manner to the heptad repeats within the RNA polymerase II CTD.
We show here that the phosphorylated CTD exists as a dynamic disordered ensemble
in solution and, by induced fit, it assumes a structured conformation when bound
to Pcf11. In addition, we detected cis-trans populations for the CTD prolines,
and found that only the all-trans form is selected for binding. These data
suggest that the recognition of the CTD is regulated by independent
site-specific modifications (phosphorylation and proline cis-trans
isomerization) and, probably, by the local concentration of suitable binding
sites.
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Selected figure(s)
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Figure 1.
Figure 1. Peptides used in this study. In the table (bottom)
the first amino acid of each peptide has been aligned to the
corresponding position within the first repeat (repeat a). The
nomenclature used in the manuscript identifies (i) the amino
acid type (ii) its number within the repeat, and (iii) the
repeat it belongs to. Phosphorylated residues are indicated in
red. A graphical representation of one heptad repeat is shown.
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Figure 6.
Figure 6. Binding of Pcf11 CID to CTD-derived peptides. (a)
1H-decoupled 1D 31P NMR spectra of YSpPTSPS (top); (YSpPTSPS)[2]
(middle); and (YSpPTSPS)[3] (bottom). The downfield peak in the
spectrum can be assigned to the 31P resonance of Ser[2a] (S[2a])
as this peak does not change substantially in the three spectra.
(b) 1H-decoupled 1D 31P NMR spectra recorded on (YSpPTSPS)[3],
alone and with increasing concentration of Pcf11(1 -142) (ratios
of 1:0, 1:1 and 1:3, top to bottom). The 31P resonances of
Ser[2b] and Ser[2c] (S[2b] and S[2c]) broaden and shift upon
protein binding, whereas Ser[2a] (S[2a]) is essentially
identical in the free and bound form. (c) Chemical shift
perturbation of Pcf11 CID upon binding to (YSpPTSPS)[2] (top)
and (YSpPTSPS)[3] (bottom). The weighted chemical shift changes
are plotted against the CID sequence. Well-dispersed resonances
in the free protein spectrum that could not be assigned in the
bound protein spectrum were given a weighted chemical shift
change value of 0.5 as default.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
144-151)
copyright 2005.
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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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B.M.Lunde,
S.L.Reichow,
M.Kim,
H.Suh,
T.C.Leeper,
F.Yang,
H.Mutschler,
S.Buratowski,
A.Meinhart,
and
G.Varani
(2010).
Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.
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Nat Struct Mol Biol,
17,
1195-1201.
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PDB codes:
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N.Jouvet,
J.Poschmann,
J.Douville,
L.Bulet,
and
D.Ramotar
(2010).
Rrd1 isomerizes RNA polymerase II in response to rapamycin.
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BMC Mol Biol,
11,
92.
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D.A.Gell,
L.Feng,
S.Zhou,
P.D.Jeffrey,
K.Bendak,
A.Gow,
M.J.Weiss,
Y.Shi,
and
J.P.Mackay
(2009).
A cis-proline in alpha-hemoglobin stabilizing protein directs the structural reorganization of alpha-hemoglobin.
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J Biol Chem,
284,
29462-29469.
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PDB code:
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M.Kim,
H.Suh,
E.J.Cho,
and
S.Buratowski
(2009).
Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7.
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J Biol Chem,
284,
26421-26426.
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S.Krishnamurthy,
M.A.Ghazy,
C.Moore,
and
M.Hampsey
(2009).
Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries.
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Mol Cell Biol,
29,
2925-2934.
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A.K.Sharma,
G.P.Zhou,
J.Kupferman,
H.K.Surks,
E.N.Christensen,
J.J.Chou,
M.E.Mendelsohn,
and
A.C.Rigby
(2008).
Probing the Interaction between the Coiled Coil Leucine Zipper of cGMP-dependent Protein Kinase I{alpha} and the C Terminus of the Myosin Binding Subunit of the Myosin Light Chain Phosphatase.
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J Biol Chem,
283,
32860-32869.
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C.R.Mandel,
Y.Bai,
and
L.Tong
(2008).
Protein factors in pre-mRNA 3'-end processing.
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Cell Mol Life Sci,
65,
1099-1122.
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L.Vasiljeva,
M.Kim,
H.Mutschler,
S.Buratowski,
and
A.Meinhart
(2008).
The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.
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Nat Struct Mol Biol,
15,
795-804.
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PDB code:
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R.Becker,
B.Loll,
and
A.Meinhart
(2008).
Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II.
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J Biol Chem,
283,
22659-22669.
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PDB codes:
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C.G.Noble,
B.Beuth,
and
I.A.Taylor
(2007).
Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.
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Nucleic Acids Res,
35,
87-99.
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PDB code:
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I.Karbat,
R.Kahn,
L.Cohen,
N.Ilan,
N.Gilles,
G.Corzo,
O.Froy,
M.Gur,
G.Albrecht,
S.H.Heinemann,
D.Gordon,
and
M.Gurevitz
(2007).
The unique pharmacology of the scorpion alpha-like toxin Lqh3 is associated with its flexible C-tail.
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FEBS J,
274,
1918-1931.
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M.Gullerova,
A.Barta,
and
Z.J.Lorkovic
(2007).
Rct1, a nuclear RNA recognition motif-containing cyclophilin, regulates phosphorylation of the RNA polymerase II C-terminal domain.
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Mol Cell Biol,
27,
3601-3611.
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P.Legrand,
N.Pinaud,
L.Minvielle-Sébastia,
and
S.Fribourg
(2007).
The structure of the CstF-77 homodimer provides insights into CstF assembly.
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Nucleic Acids Res,
35,
4515-4522.
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PDB code:
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A.Gasch,
S.Wiesner,
P.Martin-Malpartida,
X.Ramirez-Espain,
L.Ruiz,
and
M.J.Macias
(2006).
The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
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J Biol Chem,
281,
356-364.
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PDB code:
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D.Hollingworth,
C.G.Noble,
I.A.Taylor,
and
A.Ramos
(2006).
RNA polymerase II CTD phosphopeptides compete with RNA for the interaction with Pcf11.
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RNA,
12,
555-560.
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C.D.Lima
(2005).
Inducing interactions with the CTD.
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Nat Struct Mol Biol,
12,
102-103.
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D.L.Bentley
(2005).
Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.
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Curr Opin Cell Biol,
17,
251-256.
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D.P.Morris,
G.A.Michelotti,
and
D.A.Schwinn
(2005).
Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.
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J Biol Chem,
280,
31368-31377.
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M.Li,
H.P.Phatnani,
Z.Guan,
H.Sage,
A.L.Greenleaf,
and
P.Zhou
(2005).
Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1.
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Proc Natl Acad Sci U S A,
102,
17636-17641.
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PDB code:
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S.Kaneko,
and
J.L.Manley
(2005).
The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3' end formation.
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Mol Cell,
20,
91.
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Z.Zhang,
J.Fu,
and
D.S.Gilmour
(2005).
CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11.
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Genes Dev,
19,
1572-1580.
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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.
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Links
