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PDBsum entry 3ef1
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References listed in PDB file
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Key reference
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Title
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The structure of fcp1, An essential RNA polymerase ii ctd phosphatase.
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Authors
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A.Ghosh,
S.Shuman,
C.D.Lima.
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Ref.
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Mol Cell, 2008,
32,
478-490.
[DOI no: ]
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PubMed id
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Abstract
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Kinases and phosphatases regulate mRNA synthesis and processing by
phosphorylating and dephosphorylating the C-terminal domain (CTD) of the largest
subunit of RNA polymerase II. Fcp1 is an essential CTD phosphatase that
preferentially hydrolyzes Ser2-PO(4) of the tandem YSPTSPS CTD heptad array.
Fcp1 crystal structures were captured at two stages of the reaction pathway: a
Mg-BeF(3) complex that mimics the aspartylphosphate intermediate and a
Mg-AlF(4)(-) complex that mimics the transition state of the hydrolysis step.
Fcp1 is a Y-shaped protein composed of an acylphosphatase domain located at the
base of a deep canyon formed by flanking modules that are missing from the small
CTD phosphatase (SCP) clade: an Fcp1-specific helical domain and a C-terminal
BRCA1 C-terminal (BRCT) domain. The structure and mutational analysis reveals
that Fcp1 and Scp1 (a Ser5-selective phosphatase) adopt different CTD-binding
modes; we surmise the CTD threads through the Fcp1 canyon to access the active
site.
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Figure 3.
Figure 3. CTD Dephosphorylation and Close-Up Views of the
Fcp1 Active Site
(A) Two-step Fcp1 reaction pathway. Step 1
is the attack of the active-site aspartate on the phosphorus of
phospho-CTD to form an acylphosphate intermediate. Step 2
entails a nucleophilic attack by water on the acylphosphate,
resulting in formation of the inorganic phosphate product.
(B) Stereo view of the active site of Fcp1-Mg-BeF[3] complex
that mimics the acylphosphate intermediate.
(C) Stereo view
of the Fcp1-Mg-AlF[4]^− complex that mimics the step 2
transition state. Side chains are depicted in stick
representation; Mg and water are denoted by blue and red
spheres, respectively. The proposed nucleophilic water is
labeled Wat^*. Atomic contacts are indicated by dashed lines.
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Figure 5.
Figure 5. Insights to CTD Recognition
(A) Surface
representations for SpFcp1 with domains colored as in Figure 1.
A red asterisk indicates the active site Asp170-BeF[3]-Mg.
Proposed CTD path through the Fcp1 canyon is indicated by a
dashed line.
(B) Surface representation for the Scp1-CTD
complex (Zhang et al., 2006; PDB 2GHT) aligned to SpFcp1 in (A).
The S[5P]-CTD ligand is depicted as a stick model with its N and
C termini labeled. The dashed arrow indicates the CTD path on
the Scp1 surface.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Mol Cell
(2008,
32,
478-490)
copyright 2008.
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