3NGO

Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.

Wang, H.Morita, M.Yang, X.Suzuki, T.Yang, W.Wang, J.Ito, K.Wang, Q.Zhao, C.Bartlam, M.Yamamoto, T.Rao, Z.

(2010) EMBO J 

  • DOI: 10.1038/emboj.2010.152
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • CCR4, an evolutionarily conserved member of the CCR4-NOT complex, is the main cytoplasmic deadenylase. It contains a C-terminal nuclease domain with homology to the endonuclease-exonuclease-phosphatase (EEP) family of enzymes. We have determined the ...

    CCR4, an evolutionarily conserved member of the CCR4-NOT complex, is the main cytoplasmic deadenylase. It contains a C-terminal nuclease domain with homology to the endonuclease-exonuclease-phosphatase (EEP) family of enzymes. We have determined the high-resolution three-dimensional structure of the nuclease domain of CNOT6L, a human homologue of CCR4, by X-ray crystallography using the single-wavelength anomalous dispersion method. This first structure of a deadenylase belonging to the EEP family adopts a complete alpha/beta sandwich fold typical of hydrolases with highly conserved active site residues similar to APE1. The active site of CNOT6L should recognize the RNA substrate through its negatively charged surface. In vitro deadenylase assays confirm the critical active site residues and show that the nuclease domain of CNOT6L exhibits full Mg(2+)-dependent deadenylase activity with strict poly(A) RNA substrate specificity. To understand the structural basis for poly(A) RNA substrate binding, crystal structures of the CNOT6L nuclease domain have also been determined in complex with AMP and poly(A) DNA. The resulting structures suggest a molecular deadenylase mechanism involving a pentacovalent phosphate transition.


    Organizational Affiliation

    Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, PR China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT transcription complex subunit 6-like
A
398Homo sapiensMutation(s): 0 
Gene Names: CNOT6LCCR4B
EC: 3.1 (PDB Primary Data), 3.1.13.4 (UniProt)
Find proteins for Q96LI5 (Homo sapiens)
Go to UniProtKB:  Q96LI5
NIH Common Fund Data Resources
PHAROS  Q96LI5
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*A)-3'B4N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.373α = 90
b = 77.373β = 90
c = 167.177γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance