4BZC

Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Allosteric Activation of Samhd1 by Dgtp

Ji, X.Wu, Y.Yan, J.Mehrens, J.Yang, H.Delucia, M.Hao, C.Gronenborn, A.M.Skowronski, J.Ahn, J.Xiong, Y.

(2013) Nat.Struct.Mol.Biol. 20: 1304

  • DOI: 10.1038/nsmb.2692
  • Primary Citation of Related Structures:  4BZB

  • PubMed Abstract: 
  • SAMHD1, a dNTP triphosphohydrolase (dNTPase), has a key role in human innate immunity. It inhibits infection of blood cells by retroviruses, including HIV, and prevents the development of the autoinflammatory Aicardi-Goutières syndrome (AGS). The ina ...

    SAMHD1, a dNTP triphosphohydrolase (dNTPase), has a key role in human innate immunity. It inhibits infection of blood cells by retroviruses, including HIV, and prevents the development of the autoinflammatory Aicardi-Goutières syndrome (AGS). The inactive apo-SAMHD1 interconverts between monomers and dimers, and in the presence of dGTP the protein assembles into catalytically active tetramers. Here, we present the crystal structure of the human tetrameric SAMHD1-dGTP complex. The structure reveals an elegant allosteric mechanism of activation through dGTP-induced tetramerization of two inactive dimers. Binding of dGTP to four allosteric sites promotes tetramerization and induces a conformational change in the substrate-binding pocket to yield the catalytically active enzyme. Structure-based biochemical and cell-based biological assays confirmed the proposed mechanism. The SAMHD1 tetramer structure provides the basis for a mechanistic understanding of its function in HIV restriction and the pathogenesis of AGS.


    Organizational Affiliation

    1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
A, B, C, D
550Homo sapiensGene Names: SAMHD1 (MOP5)
EC: 3.1.5.-
Find proteins for Q9Y3Z3 (Homo sapiens)
Go to Gene View: SAMHD1
Go to UniProtKB:  Q9Y3Z3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
T8T
Query on T8T

Download SDF File 
Download CCD File 
A, B, C, D
2'-deoxyguanosine-5'-O-(1-thiotriphosphate)
C10 H16 N5 O12 P3 S
IOCRYHATDKHWPM-KUFCIHQDSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.002α = 90.00
b = 138.727β = 113.56
c = 93.715γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2013-11-20
    Type: Database references