4XQ0

Structure of fission yeast RNA polymerase II CTD phosphatase Fcp1-R271A bound to beryllium fluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1.

Schwer, B.Ghosh, A.Sanchez, A.M.Lima, C.D.Shuman, S.

(2015) Rna 21: 1135-1146

  • DOI: 10.1261/rna.050286.115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein phosphatases regulate mRNA synthesis and processing by remodeling the carboxy-terminal domain (CTD) of RNA polymerase II (Pol2) to dynamically inscribe a Pol2 CTD code. Fission yeast Fcp1 (SpFcp1) is an essential 723-amino acid CTD phosphatas ...

    Protein phosphatases regulate mRNA synthesis and processing by remodeling the carboxy-terminal domain (CTD) of RNA polymerase II (Pol2) to dynamically inscribe a Pol2 CTD code. Fission yeast Fcp1 (SpFcp1) is an essential 723-amino acid CTD phosphatase that preferentially hydrolyzes Ser2-PO4 of the YS(2)PTSPS repeat. The SpFcp1 catalytic domain (aa 140-580) is composed of a DxDxT acyl-phosphatase module (FCPH) and a BRCT module. Here we conducted a genetic analysis of SpFcp1, which shows that (i) phosphatase catalytic activity is required for vegetative growth of fission yeast; (ii) the flanking amino-terminal domain (aa 1-139) and its putative metal-binding motif C(99)H(101)Cys(109)C(112) are essential; (iii) the carboxy-terminal domain (aa 581-723) is dispensable; (iv) a structurally disordered internal segment of the FCPH domain (aa 330-393) is dispensable; (v) lethal SpFcp1 mutations R271A and R299A are rescued by shortening the Pol2 CTD repeat array; and (vi) CTD Ser2-PO4 is not the only essential target of SpFcp1 in vivo. Recent studies highlight a second CTD code involving threonine phosphorylation of a repeat motif in transcription elongation factor Spt5. We find that Fcp1 can dephosphorylate Thr1-PO4 of the fission yeast Spt5 CTD nonamer repeat T(1)PAWNSGSK. We identify Arg271 as a governor of Pol2 versus Spt5 CTD substrate preference. Our findings implicate Fcp1 as a versatile sculptor of both the Pol2 and Spt5 CTD codes. Finally, we report a new 1.45 Å crystal structure of SpFcp1 with Mg(2+) and AlF3 that mimics an associative phosphorane transition state of the enzyme-aspartyl-phosphate hydrolysis reaction.


    Organizational Affiliation

    Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit A C-terminal domain phosphatase
A
372Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 1 
Gene Names: fcp1
EC: 3.1.3.16
Find proteins for Q9P376 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P376
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.422α = 90.00
b = 80.255β = 90.00
c = 89.196γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-18 
  • Released Date: 2015-03-04 
  • Deposition Author(s): Ghosh, A., Lima, C.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM061906

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy