6XU1

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.

Morris, E.R.Caswell, S.J.Kunzelmann, S.Arnold, L.H.Purkiss, A.G.Kelly, G.Taylor, I.A.

(2020) Nat Commun 11: 3165-3165

  • DOI: https://doi.org/10.1038/s41467-020-16983-2
  • Primary Citation of Related Structures:  
    6TX0, 6TXA, 6TXC, 6TXE, 6TXF, 6XU1, 6YOM

  • PubMed Abstract: 

    SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4 + myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the P α -O 5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.


  • Organizational Affiliation

    Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D, E
A, B, C, D, E, F, G, H
520Homo sapiensMutation(s): 1 
Gene Names: SAMHD1MOP5
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
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
BA [auth C]
FB [auth G]
JA [auth D]
MB [auth H]
N [auth A]
BA [auth C],
FB [auth G],
JA [auth D],
MB [auth H],
N [auth A],
QA [auth E],
RA [auth E],
U [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
DZ4 (Subject of Investigation/LOI)
Query on DZ4

Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth C]
DA [auth D]
EB [auth G]
GB [auth H]
AA [auth C],
CA [auth C],
DA [auth D],
EB [auth G],
GB [auth H],
IA [auth D],
LB [auth H],
M [auth A],
O [auth A],
PA [auth E],
SA [auth E],
T [auth B],
V [auth C],
XA [auth F],
YA [auth F],
ZA [auth G]
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
C10 H17 N6 O11 P3
WKIPJDSLGCBQCU-RRKCRQDMSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AB [auth G]
EA [auth D]
HB [auth H]
I [auth A]
LA [auth E]
AB [auth G],
EA [auth D],
HB [auth H],
I [auth A],
LA [auth E],
P [auth B],
TA [auth F],
W [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BB [auth G]
CB [auth G]
DB [auth G]
FA [auth D]
GA [auth D]
BB [auth G],
CB [auth G],
DB [auth G],
FA [auth D],
GA [auth D],
HA [auth D],
IB [auth H],
J [auth A],
JB [auth H],
K [auth A],
KA [auth D],
KB [auth H],
L [auth A],
MA [auth E],
NA [auth E],
OA [auth E],
Q [auth B],
R [auth B],
S [auth B],
UA [auth F],
VA [auth F],
WA [auth F],
X [auth C],
Y [auth C],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.369α = 90
b = 171.86β = 90
c = 179.572γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom108014/Z/15/Z
Wellcome TrustUnited KingdomFC001029
Medical Research Council (MRC, United Kingdom)United KingdomFC001029
Cancer Research UKUnited KingdomFC001029

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description