4H3H

Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72.

Xiang, K.Manley, J.L.Tong, L.

(2012) Genes Dev. 26: 2265-2270

  • DOI: 10.1101/gad.198853.112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ssu72, an RNA polymerase II C-terminal domain (CTD) phospho-Ser5 (pSer5) phosphatase, was recently reported to have pSer7 phosphatase activity as well. We report here the crystal structure of a ternary complex of the N-terminal domain of human symple ...

    Ssu72, an RNA polymerase II C-terminal domain (CTD) phospho-Ser5 (pSer5) phosphatase, was recently reported to have pSer7 phosphatase activity as well. We report here the crystal structure of a ternary complex of the N-terminal domain of human symplekin, human Ssu72, and a 10-mer pSer7 CTD peptide. Surprisingly, the peptide is bound in the Ssu72 active site with its backbone running in the opposite direction compared with a pSer5 peptide. The pSer7 phosphatase activity of Ssu72 is ∼4000-fold lower than its pSer5 phosphatase activity toward a peptide substrate, consistent with the structural observations.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Symplekin
A, D
351Homo sapiensMutation(s): 0 
Gene Names: SYMPK (SPK)
Find proteins for Q92797 (Homo sapiens)
Go to Gene View: SYMPK
Go to UniProtKB:  Q92797
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit A C-terminal domain phosphatase SSU72
B, E
214Homo sapiensMutation(s): 1 
Gene Names: SSU72
EC: 3.1.3.16
Find proteins for Q9NP77 (Homo sapiens)
Go to Gene View: SSU72
Go to UniProtKB:  Q9NP77
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pol II CTD peptide
F
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
F
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.819α = 90.00
b = 97.742β = 98.63
c = 104.603γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-09-13 
  • Released Date: 2012-10-31 
  • Deposition Author(s): Xiang, K., Tong, L.

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description