2GHQ

CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1.

Zhang, Y.Kim, Y.Genoud, N.Gao, J.Kelly, J.W.Pfaff, S.L.Gill, G.N.Dixon, J.E.Noel, J.P.

(2006) Mol Cell 24: 759-770

  • DOI: 10.1016/j.molcel.2006.10.027
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fc ...

    Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.


    Organizational Affiliation

    Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037. Electronic address: noel@salk.edu.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II largest subunitC, D9Homo sapiensMutation(s): 2 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (UniProt)
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
NIH Common Fund Data Resources
PHAROS  P24928
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1A, B181Homo sapiensMutation(s): 1 
Gene Names: CTDSP1NIF3NLIIFSCP1
EC: 3.1.3.16
Find proteins for Q9GZU7 (Homo sapiens)
Explore Q9GZU7 
Go to UniProtKB:  Q9GZU7
NIH Common Fund Data Resources
PHAROS  Q9GZU7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C,DL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.067α = 90
b = 78.813β = 112.17
c = 62.992γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-03-27 
  • Released Date: 2006-12-05 
  • Deposition Author(s): Zhang, Y., Noel, J.P.

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance