3TDB

Human Pin1 bound to trans peptidomimetic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.267 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Kinetic Analysis of Prolyl-isomerization/Phosphorylation Cross-Talk in the CTD Code.

Zhang, M.Wang, X.J.Chen, X.Bowman, M.E.Luo, Y.Noel, J.P.Ellington, A.D.Etzkorn, F.A.Zhang, Y.

(2012) Acs Chem.Biol. 7: 1462-1470

  • DOI: 10.1021/cb3000887
  • Primary Citation of Related Structures:  3TCZ

  • PubMed Abstract: 
  • The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation ...

    The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A
158Homo sapiensGene Names: PIN1
EC: 5.2.1.8
Find proteins for Q13526 (Homo sapiens)
Go to Gene View: PIN1
Go to UniProtKB:  Q13526
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download SDF File 
Download CCD File 
A
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
3TB
Query on 3TB

Download SDF File 
Download CCD File 
A
N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-amino-5-carbamimidamido-1-oxopentan-2-yl]carbamoyl}cyclopentylidene]-3-(phosphonooxy)propan-2-yl]-L-phenylalaninamide
C24 H38 N7 O7 P
UFUNWHANDTZFCQ-BELXZNSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.267 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.273α = 90.00
b = 69.273β = 90.00
c = 79.657γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-08-10 
  • Released Date: 2012-06-27 
  • Deposition Author(s): Zhang, M., Zhang, Y.

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-09-05
    Type: Database references