2GHT

CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II

• PDB DOI:  https://doi.org/10.2210/pdb2GHT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-27 Released: 2006-12-05 
• Deposition Author(s): Zhang, Y., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.216 
• R-Value Observed: 0.242 

Literature

Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1.

Zhang, Y., Kim, Y., Genoud, N., Gao, J., Kelly, J.W., Pfaff, S.L., Gill, G.N., Dixon, J.E., Noel, J.P.

(2006) Mol Cell 24: 759-770

• PubMed: 17157258 
• DOI: https://doi.org/10.1016/j.molcel.2006.10.027
• Primary Citation of Related Structures:  
  2GHQ, 2GHT


• PubMed Abstract: 
  

Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.61 kDa 
• Atom Count: 3,274 
• Modelled Residue Count: 373 
• Deposited Residue Count: 378 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1	A, B	181	Homo sapiens	Mutation(s): 1  Gene Names: CTDSP1, NIF3, NLIIF, SCP1 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II largest subunit	C, D	8	Homo sapiens	Mutation(s): 1  Gene Names: POLR2A, POLR2 EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens) Explore P24928  Go to UniProtKB:  P24928
PHAROS:  P24928

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.216 
• R-Value Observed: 0.242 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.916	α = 90
b = 78.787	β = 112.08
c = 62.948	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
XDS	data reduction
AMoRE	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Zhang, Y., Noel, J.P.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description