4QG0

Crystal structure of the tetrameric dGTP/dUTP-bound SAMHD1 (RN206) mutant catalytic core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates.

Koharudin, L.M.Wu, Y.DeLucia, M.Mehrens, J.Gronenborn, A.M.Ahn, J.

(2014) J Biol Chem 289: 32617-32627

  • DOI: 10.1074/jbc.M114.591958
  • Primary Citation of Related Structures:  
    4QFX, 4QFY, 4QFZ, 4QG0, 4QG1, 4QG2, 4QG4

  • PubMed Abstract: 
  • Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) plays a critical role in inhibiting HIV infection, curtailing the pool of dNTPs available for reverse transcription of the viral genome. Recent structural data suggested a compelling mechanism for the regulation of SAMHD1 enzymatic activity and revealed dGTP-induced association of two inactive dimers into an active tetrameric enzyme ...

    Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) plays a critical role in inhibiting HIV infection, curtailing the pool of dNTPs available for reverse transcription of the viral genome. Recent structural data suggested a compelling mechanism for the regulation of SAMHD1 enzymatic activity and revealed dGTP-induced association of two inactive dimers into an active tetrameric enzyme. Here, we present the crystal structures of SAMHD1 catalytic core (residues 113-626) tetramers, complexed with mixtures of nucleotides, including dGTP/dATP, dGTP/dCTP, dGTP/dTTP, and dGTP/dUTP. The combined structural and biochemical data provide insight into dNTP promiscuity at the secondary allosteric site and how enzymatic activity is modulated. In addition, we present biochemical analyses of GTP-induced SAMHD1 full-length tetramerization and the structure of SAMHD1 catalytic core tetramer in complex with GTP/dATP, revealing the structural basis of GTP-mediated SAMHD1 activation. Altogether, the data presented here advance our understanding of SAMHD1 function during cellular homeostasis.


    Organizational Affiliation

    From the Department of Structural Biology and Pittsburgh Center for HIV-Host Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260 jia12@pitt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1A, B, C, D550Homo sapiensMutation(s): 2 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGT
Query on DGT

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
T [auth D]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
DUT
Query on DUT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B],
M [auth B],
O [auth C],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
O [auth C],
Q [auth C],
S [auth D],
U [auth D]
DEOXYURIDINE-5'-TRIPHOSPHATE
C9 H15 N2 O14 P3
AHCYMLUZIRLXAA-SHYZEUOFSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
X [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
N [auth B],
R [auth C],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
R [auth C],
V [auth D],
W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.856α = 90
b = 146.596β = 114.62
c = 98.686γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Database references