4YGY

Crystal Structure of Human Scp1 bound to trans-proline peptidomimetic CTD phospho-Ser5 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1021/acschembio.5b00296
  • Primary Citation of Related Structures:  
    4YGX, 4YGY, 4YH1

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
A, B
189Homo sapiensMutation(s): 1 
Gene Names: CTDSP1NIF3NLIIFSCP1
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZU7 (Homo sapiens)
Explore Q9GZU7 
Go to UniProtKB:  Q9GZU7
PHAROS:  Q9GZU7
GTEx:  ENSG00000144579 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZU7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptidomimetic CTD phospho-Ser5 peptide
C, D
12synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.28α = 90
b = 78.335β = 112.59
c = 63.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Derived calculations
  • Version 1.2: 2015-10-28
    Changes: Database references