7A5Y

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p - and S p -dNTP alpha S Diastereomers.

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

(2021) Biochemistry 60: 1682-1698

  • DOI: https://doi.org/10.1021/acs.biochem.0c00944
  • Primary Citation of Related Structures:  
    7A5Y

  • PubMed Abstract: 

    SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4 + myeloid lineage and resting T-cells. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome (AGS) and certain cancers. More recently, SAMHD1 has been linked to anticancer drug resistance and the suppression of the interferon response to cytosolic nucleic acids after DNA damage. Here, we probe dNTP hydrolysis and inhibition of SAMHD1 using the R p and S p diastereomers of dNTPαS nucleotides. Our biochemical and enzymological data show that the α-phosphorothioate substitution in S p -dNTPαS but not R p -dNTPαS diastereomers prevents Mg 2+ ion coordination at both the allosteric and catalytic sites, rendering SAMHD1 unable to form stable, catalytically active homotetramers or hydrolyze substrate dNTPs at the catalytic site. Furthermore, we find that S p -dNTPαS diastereomers competitively inhibit dNTP hydrolysis, while R p -dNTPαS nucleotides stabilize tetramerization and are hydrolyzed with similar kinetic parameters to cognate dNTPs. For the first time, we present a cocrystal structure of SAMHD1 with a substrate, R p -dGTPαS, in which an Fe-Mg-bridging water species is poised for nucleophilic attack on the P α . We conclude that it is the incompatibility of Mg 2+ , a hard Lewis acid, and the α-phosphorothioate thiol, a soft Lewis base, that prevents the S p -dNTPαS nucleotides coordinating in a catalytically productive conformation. On the basis of these data, we present a model for SAMHD1 stereospecific hydrolysis of R p -dNTPαS nucleotides and for a mode of competitive inhibition by S p -dNTPαS nucleotides that competes with formation of the enzyme-substrate complex.


  • Organizational Affiliation

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


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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T8T (Subject of Investigation/LOI)
Query on T8T

Download Ideal Coordinates CCD File 
AB [auth F]
CA [auth C]
DA [auth C]
EA [auth D]
EB [auth G]
AB [auth F],
CA [auth C],
DA [auth C],
EA [auth D],
EB [auth G],
FA [auth D],
FB [auth G],
GB [auth H],
HB [auth H],
JA [auth D],
L [auth A],
LB [auth H],
N [auth A],
OA [auth E],
P [auth A],
PA [auth E],
Q [auth B],
R [auth B],
RA [auth E],
SA [auth F],
TA [auth F],
V [auth B],
X [auth B],
YA [auth F]
2'-deoxyguanosine-5'-O-(1-thiotriphosphate)
C10 H16 N5 O12 P3 S
IOCRYHATDKHWPM-KUFCIHQDSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
BB [auth G]
GA [auth D]
I [auth A]
IB [auth H]
KA [auth E]
BB [auth G],
GA [auth D],
I [auth A],
IB [auth H],
KA [auth E],
S [auth B],
UA [auth F],
Z [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CB [auth G]
DB [auth G]
HA [auth D]
AA [auth C],
BA [auth C],
CB [auth G],
DB [auth G],
HA [auth D],
IA [auth D],
J [auth A],
JB [auth H],
K [auth A],
KB [auth H],
LA [auth E],
M [auth A],
MA [auth E],
NA [auth E],
O [auth A],
QA [auth E],
T [auth B],
U [auth B],
VA [auth F],
W [auth B],
WA [auth F],
XA [auth F],
Y [auth C],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.193α = 90
b = 181.263β = 90
c = 286.331γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom108014/Z/15/Z
Wellcome TrustUnited KingdomFC001178
Medical Research Council (MRC, United Kingdom)United KingdomFC001178
Cancer Research UKUnited KingdomFC001178

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description