PDBsum entry 3ef0

Hydrolase

PDB id: 3ef0

Contents

Protein chain

361 a.a. *

Ligands

ALF

Metals

_MG

Waters ×175

* Residue conservation analysis

PDB id:

3ef0

Name:

Hydrolase

Title:

The structure of fcp1, an essential RNA polymerase ii ctd phosphatase

Structure:

RNA polymerase ii subunit a c-terminal domain phosphatase. Chain: a. Fragment: fcp1 homology domain, catalytically active fragment, unp residues 149-580. Synonym: ctd phosphatase fcp1. Engineered: yes

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: fcp1, spac19b12.05c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.220 R-free: 0.252

Authors:

A.Ghosh,C.D.Lima

Key ref:

A.Ghosh et al. (2008). The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Mol Cell, 32, 478-490. PubMed id: 19026779 DOI: 10.1016/j.molcel.2008.09.021

Date:

07-Sep-08 Release date: 02-Dec-08

Protein chain

Q9P376  (FCP1_SCHPO) -  RNA polymerase II subunit A C-terminal domain phosphatase from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 723 a.a.

Struc: 361 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.16 - protein-serine/threonine phosphatase.
• Reaction:
  1. O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate
  2. O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.molcel.2008.09.021

Mol Cell 32:478-490 (2008)

PubMed id: 19026779

The structure of Fcp1, an essential RNA polymerase II CTD phosphatase.

A.Ghosh, S.Shuman, C.D.Lima.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 32, 478-490) copyright 2008.

Figures were selected by the author.