5YHW

Crystal structure of Pig SAMHD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

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Literature

Structural characterization and directed modification of Sus scrofa SAMHD1 reveal the mechanism underlying deoxynucleotide regulation.

Kong, J.Wang, M.M.He, S.Y.Peng, X.Qin, X.H.

(2019) FEBS J 286: 3844-3857

  • DOI: https://doi.org/10.1111/febs.14943
  • Primary Citation of Related Structures:  
    5YHW

  • PubMed Abstract: 

    Sterile α-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) is an intrinsic antiviral restriction factor known to play a vital role in preventing multiple viral infections and in the control of the cellular deoxynucleoside triphosphate (dNTP) pool. Human and mouse SAMHD1 have both been extensively studied; however, our knowledge on porcine SAMHD1 is limited. Here, we report our findings from comprehensive structural and functional studies on porcine SAMHD1. We determined the crystal structure of porcine SAMHD1 and showed that it forms a symmetric tetramer. Moreover, we modified the deoxynucleotide triphosphohydrolase (dNTPase) activity of SAMHD1 by site-directed mutagenesis based on the crystal structure, and obtained an artificial dimeric enzyme possessing high dNTPase activity. Taken together, our results define the mechanism underlying dNTP regulation and provide a deeper understanding of the regulation of porcine SAMHD1 functions. Directed modification of key residues based on the protein structure enhances the activity of the enzyme, which will be beneficial in the search for new antiviral strategies and for future translational applications.


  • Organizational Affiliation

    School of Chemical Engineering and Technology, Tianjin University, China.


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
524Sus scrofaMutation(s): 2 
Gene Names: SAMHD1
UniProt
Find proteins for I3LG77 (Sus scrofa)
Explore I3LG77 
Go to UniProtKB:  I3LG77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LG77
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT (Subject of Investigation/LOI)
Query on DGT

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth D]
DA [auth E]
FA [auth E]
GA [auth E]
AA [auth D],
CA [auth D],
DA [auth E],
FA [auth E],
GA [auth E],
I [auth A],
IA [auth F],
JA [auth F],
K [auth A],
L [auth A],
MA [auth G],
O [auth B],
OA [auth G],
P [auth B],
QA [auth G],
R [auth B],
RA [auth H],
S [auth C],
TA [auth H],
U [auth C],
VA [auth H],
W [auth C],
X [auth C],
Y [auth D]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
EA [auth E]
HA [auth E]
J [auth A]
KA [auth F]
BA [auth D],
EA [auth E],
HA [auth E],
J [auth A],
KA [auth F],
LA [auth G],
M [auth A],
N [auth B],
NA [auth G],
PA [auth G],
Q [auth B],
SA [auth H],
T [auth C],
UA [auth H],
V [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.54α = 78.66
b = 95.909β = 88.12
c = 130.749γ = 82.68
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXdata reduction
PHENIXdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31400465

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description