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PDBsum entry 3d9n
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Transcription
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PDB id
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3d9n
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References listed in PDB file
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Key reference
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Title
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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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Authors
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R.Becker,
B.Loll,
A.Meinhart.
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Ref.
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J Biol Chem, 2008,
283,
22659-22669.
[DOI no: ]
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PubMed id
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Abstract
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Concomitant with RNA polymerase II (Pol II) transcription, RNA maturation
factors are recruited to the carboxyl-terminal domain (CTD) of Pol II, whose
phosphorylation state changes during a transcription cycle. CTD phosphorylation
triggers recruitment of functionally different factors involved in RNA
processing and transcription termination; most of these factors harbor a
conserved CTD interacting domain (CID). Orchestration of factor recruitment is
believed to be conducted by CID recognition of distinct phosphorylated forms of
the CTD. We show that the human RNA processing factor SCAF8 interacts weakly
with the unphosphorylated CTD of Pol II. Upon phosphorylation, affinity for the
CTD is increased; however, SCAF8 is promiscuous to the phosphorylation pattern
on the CTD. Employing a combined structural and biophysical approach, we were
able to distinguish motifs within CIDs that are involved in a generic CTD
sequence recognition from items that confer phospho-specificity.
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Figure 1.
FIGURE 1. SCAF8-CID binding to different phosphorylated
forms of the CTD measured by fluorescence anisotropy competition
titration experiments. Data points of the reference measurement
of SCAF8-CID titrated to 2 µM FAM-Ser(P)-2-CTD peptide are
presented as filled circles (  ). Data points for
competition experiments where 100 µM concentrations of
different non-fluorescently labeled CTD peptides competed
against 2 µM FAM-Ser(P)-2-CTD peptide are given as open
symbols. Fluorescence anisotropy data using
Ser(P)-2/Ser(P)-5-CTD peptide are presented as open diamonds (
 )
(K[d] = 19 (+/- 2/2) µM), Ser(P)-2-CTD peptide as open
circles ( ) (K[d] = 68 (+/- 8/6)
µM), Ser(P)-2/Ser(P)-7-CTD as open squares (  ) (K[d] =
90 (+/- 4/3) µM), and Ser(P)-5-CTD as inverted open
triangles (  ) (K[d] = 330 (+/-
50/30) µM). The lines represent the best fit to data of
individual measurements.
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Figure 3.
FIGURE 3. A gallery of SCAF8-CID binding to different
phospho forms of the CTD. SCAF8-CID is shown as a ribbon
representation; the CTD is shown as a stick model. Hydrogen
bonds between SCAF8-CID and the CTD are illustrated as black
dashed lines, and intramolecular hydrogen bonds within the
β-turn of the CTD are in orange. 2F[o] - F[c] electron density
contoured at 0.9  for the bound
CTD-peptides is illustrated beneath each model. Shown is
SCAF8-CID binding Ser(P)-2/Ser(P)-5-CTD (PDB code 3D9K) (A),
Ser(P)-2-CTD (PDB code 3D9L) (B), Ser(P)-5-CTD (PDB code 3D9M)
(C), unphosphorylated CTD (PDB code 3D9O) (D), and
Ser(P)-2/Ser(P)-7-CTD (PDB code 3D9N) (E) and Pcf11-CID (PDB
code 1SZA) binding Ser(P)-2-CTD (F).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
22659-22669)
copyright 2008.
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