5AO1

Crystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddGTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.

Arnold, L.H.Groom, H.C.T.Kunzelmann, S.Schwefel, D.Caswell, S.J.Ordonez, P.Mann, M.C.Rueschenbaum, S.Goldstone, D.C.Pennell, S.Howell, S.A.Stoye, J.P.Webb, M.Taylor, I.A.Bishop, K.N.

(2015) PLoS Pathog 11: 5194

  • DOI: https://doi.org/10.1371/journal.ppat.1005194
  • Primary Citation of Related Structures:  
    5AO0, 5AO1, 5AO2, 5AO3, 5AO4

  • PubMed Abstract: 

    SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells. Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function, although alternative mechanisms have been proposed recently. Here, we present combined structural and virological data demonstrating that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form "long-lived" enzymatically competent tetramers. Tetramer disruption invariably abolishes restriction but has varied effects on in vitro triphosphohydrolase activity. SAMHD1 phosphorylation also ablates restriction and tetramer formation but without affecting triphosphohydrolase steady-state kinetics. However phospho-SAMHD1 is unable to catalyse dNTP turnover under conditions of nucleotide depletion. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity where dephosphorylation switches housekeeping SAMHD1 found in cycling cells to a high-activity stable tetrameric form that depletes and maintains low levels of dNTPs in differentiated cells.


  • Organizational Affiliation

    The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
A, B, C, D
491Homo sapiensMutation(s): 0 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG3
Query on DG3

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
K [auth B]
L [auth B]
P [auth C]
F [auth A],
H [auth B],
K [auth B],
L [auth B],
P [auth C],
Q [auth D],
T [auth D],
U [auth D]
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
S [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B],
N [auth B],
R [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.121α = 90
b = 187.356β = 100.54
c = 81.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary