3PGL

Crystal structure of human small C-terminal domain phosphatase 1 (Scp1) bound to rabeprazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor.

Zhang, M.Cho, E.J.Burstein, G.Siegel, D.Zhang, Y.

(2011) Acs Chem.Biol. 6: 511-519

  • DOI: 10.1021/cb100357t

  • PubMed Abstract: 
  • The unstructured C-terminal domain (CTD) of eukaryotic RNA polymerase II dynamically regulates the process of transcription by recruiting different factors to nascent mRNA through its multiple phosphorylation patterns. A newly discovered class of pho ...

    The unstructured C-terminal domain (CTD) of eukaryotic RNA polymerase II dynamically regulates the process of transcription by recruiting different factors to nascent mRNA through its multiple phosphorylation patterns. A newly discovered class of phosphatases, the human small C-terminal domain phosphatases (Scp's), specifically dephosphorylates phosphorylated Ser(5) (phospho.Ser5) of the tandem heptad repeats of the CTD of RNA polymerase II. Scp's also function as transcription regulators that epigenetically silence the expression of specific neuronal genes, whose inactivation leads to neuronal stem cell differentiation. Small molecule inhibitors of Scp's will be valuable for elucidating their mechanism in nervous system development and can possibly offer new strategies to treat diseases related to neurodegeneration. Despite the difficulty in developing selective inhibitors of protein phosphatases, we have recognized a characteristic hydrophobic binding pocket adjacent to the active site in Scp's that may facilitate selective inhibition. In the present study, we successfully identified the first selective lead compound, rabeprazole, for the Scp/TFIIF-interacting CTD phosphatase (Fcp) family. The high-resolution crystal structure of rabeprazole-bound Scp1 showed that the compound indeed binds to the hydrophobic binding pocket. We further confirmed that rabeprazole only targets Scp's but not its close family members Fcp1 and Dullard or bacteriophage λ Ser/Thr phosphatase. Such specificity may prove important for In Vivo studies since accidental inhibition of Fcp1 or Dullard would result in cell malfunctions and even cell death.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
A, B
180Homo sapiensMutation(s): 0 
Gene Names: CTDSP1 (NIF3, NLIIF, SCP1)
EC: 3.1.3.16
Find proteins for Q9GZU7 (Homo sapiens)
Go to Gene View: CTDSP1
Go to UniProtKB:  Q9GZU7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RZX
Query on RZX

Download SDF File 
Download CCD File 
A
2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole
Rabeprazole
C18 H21 N3 O3 S
YREYEVIYCVEVJK-RUZDIDTESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RZXKi: 5000 nM BINDINGMOAD
RZXKi: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.525α = 90.00
b = 78.260β = 111.93
c = 62.682γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description