4BZB

Crystal structure of the tetrameric dGTP-bound SAMHD1 mutant catalytic core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1038/nsmb.2692
  • Primary Citation of Related Structures:  
    4BZB, 4BZC

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
A, B, C, D
550Homo sapiensMutation(s): 2 
EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens)
Explore Q9Y3Z3 
Go to UniProtKB:  Q9Y3Z3
PHAROS:  Q9Y3Z3
GTEx:  ENSG00000101347 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT
Query on DGT

Download Ideal Coordinates CCD File 
E [auth A]
G [auth A]
I [auth A]
J [auth B]
L [auth B]
E [auth A],
G [auth A],
I [auth A],
J [auth B],
L [auth B],
N [auth B],
O [auth C],
Q [auth C],
S [auth C],
T [auth D],
V [auth D],
X [auth D]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
H [auth A]
K [auth B]
M [auth B]
P [auth C]
F [auth A],
H [auth A],
K [auth B],
M [auth B],
P [auth C],
R [auth C],
U [auth D],
W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.203α = 90
b = 146.746β = 114.42
c = 98.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description