7LU5

SAMHD1(113-626) H206R D207N R366H

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2021-02-20 Released: 2021-11-24 
  • Deposition Author(s): Temple, J.T., Bowen, N.E.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins.

Bowen, N.E.Temple, J.Shepard, C.Oo, A.Arizaga, F.Kapoor-Vazirani, P.Persaud, M.Yu, C.H.Kim, D.H.Schinazi, R.F.Ivanov, D.N.Diaz-Griffero, F.Yu, D.S.Xiong, Y.Kim, B.

(2021) J Biol Chem 297: 101170-101170

  • DOI: https://doi.org/10.1016/j.jbc.2021.101170
  • Primary Citation of Related Structures:  
    7LTT, 7LU5

  • PubMed Abstract: 

    Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.


  • Organizational Affiliation

    Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA.


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, I, J, K, L, M, N, O, P
535Homo sapiensMutation(s): 3 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT (Subject of Investigation/LOI)
Query on DGT

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
CA [auth F]
DA [auth G]
EA [auth G]
AA [auth E],
BA [auth F],
CA [auth F],
DA [auth G],
EA [auth G],
FA [auth H],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth J],
KA [auth J],
LA [auth K],
MA [auth K],
NA [auth L],
OA [auth M],
PA [auth M],
Q [auth A],
QA [auth N],
R [auth A],
RA [auth O],
S [auth A],
SA [auth O],
T [auth B],
TA [auth O],
U [auth B],
UA [auth P],
V [auth C],
VA [auth P],
W [auth C],
X [auth D],
Y [auth E],
Z [auth E]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.73α = 90
b = 573.482β = 114.72
c = 100.501γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI136737
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI136581
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI150451
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA254403
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124165

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description