4YGX

Crystal Structure of D. melanogaster Ssu72+Symplekin bound to cis peptidomimetic CTD phospho-Ser5 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II.

Mayfield, J.E.Fan, S.Wei, S.Zhang, M.Li, B.Ellington, A.D.Etzkorn, F.A.Zhang, Y.J.

(2015) Acs Chem.Biol. 10: 2405-2414

  • DOI: 10.1021/acschembio.5b00296
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using ...

    Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using novel, direct, and quantitative chemical tools. We determine the proline isomeric preference of three CTD phosphatases: Ssu72 as cis-proline specific, Scp1 and Fcp1 as strongly trans-preferred. Due to this inherent characteristic, these phosphatases respond differently to enzymes that catalyze the isomerization of proline, like Ess1/Pin1. We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. This leads to diversified phosphorylation states of CTD in vitro and in cells. We provide the chemical tools to investigate proline isomerization and its ability to selectively enhance signaling in transcription and other biological contexts.


    Organizational Affiliation

    Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Symplekin
A, C
339Drosophila melanogasterMutation(s): 0 
Gene Names: Sym
Find proteins for Q8MSU4 (Drosophila melanogaster)
Go to UniProtKB:  Q8MSU4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LD40846p
B, D
200Drosophila melanogasterMutation(s): 2 
Gene Names: Ssu72 (BEST:CK01830, Dmel\CG14216, dSsu72)
EC: 3.1.3.-, 3.1.3.16, 3.1.3.41
Find proteins for Q9VWE4 (Drosophila melanogaster)
Go to UniProtKB:  Q9VWE4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
cis peptidomimetic CTD phospho-Ser5 peptide
E
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E
NON-POLYMERH2 N

--

4CG
Query on 4CG
E
peptide linkingC9 H16 N O6 P

--

ACE
Query on ACE
E
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 127.880α = 90.00
b = 127.880β = 90.00
c = 105.861γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references