1TA0

Three-dimensional structure of a RNA-polymerase II binding protein with associated ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Mechanism of RNA Polymerase II CTD Phosphatases.

Kamenski, T.Heilmeier, S.Meinhart, T.Cramer, P.

(2004) Mol.Cell 15: 399-407

  • DOI: 10.1016/j.molcel.2004.06.035
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recycling of RNA polymerase II (Pol II) after transcription requires dephosphorylation of the polymerase C-terminal domain (CTD) by the phosphatase Fcp1. We report the X-ray structure of the small CTD phosphatase Scp1, which is homologous to the Fcp1 ...

    Recycling of RNA polymerase II (Pol II) after transcription requires dephosphorylation of the polymerase C-terminal domain (CTD) by the phosphatase Fcp1. We report the X-ray structure of the small CTD phosphatase Scp1, which is homologous to the Fcp1 catalytic domain. The structure shows a core fold and an active center similar to those of phosphotransferases and phosphohydrolases that solely share a DXDX(V/T) signature motif with Fcp1/Scp1. We demonstrate that the first aspartate in the signature motif undergoes metal-assisted phosphorylation during catalysis, resulting in a phosphoaspartate intermediate that was structurally mimicked with the inhibitor beryllofluoride. Specificity may result from CTD binding to a conserved hydrophobic pocket between the active site and an insertion domain that is unique to Fcp1/Scp1. Fcp1 specificity may additionally arise from phosphatase recruitment near the CTD via the Pol II subcomplex Rpb4/7, which is shown to be required for binding of Fcp1 to the polymerase in vitro.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
A
197Homo sapiensMutation(s): 0 
Gene Names: CTDSP1 (NIF3, NLIIF, SCP1)
EC: 3.1.3.16
Find proteins for Q9GZU7 (Homo sapiens)
Go to Gene View: CTDSP1
Go to UniProtKB:  Q9GZU7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-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: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.820α = 90.00
b = 47.170β = 90.00
c = 40.070γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSphasing
XDSdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance