5AO4

Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues 115-626) bound to GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.

Arnold, L.H.Groom, H.C.T.Kunzelmann, S.Schwefel, D.Caswell, S.J.Ordonez, P.Mann, M.C.Rueschenbaum, S.Goldstone, D.C.Pennell, S.Howell, S.A.Stoye, J.P.Webb, M.Taylor, I.A.Bishop, K.N.

(2015) Plos Pathog. 11: 5194

  • DOI: 10.1371/journal.ppat.1005194
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells. Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function, ...

    SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells. Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function, although alternative mechanisms have been proposed recently. Here, we present combined structural and virological data demonstrating that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form "long-lived" enzymatically competent tetramers. Tetramer disruption invariably abolishes restriction but has varied effects on in vitro triphosphohydrolase activity. SAMHD1 phosphorylation also ablates restriction and tetramer formation but without affecting triphosphohydrolase steady-state kinetics. However phospho-SAMHD1 is unable to catalyse dNTP turnover under conditions of nucleotide depletion. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity where dephosphorylation switches housekeeping SAMHD1 found in cycling cells to a high-activity stable tetrameric form that depletes and maintains low levels of dNTPs in differentiated cells.


    Organizational Affiliation

    The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
A, B, C, D
538Homo sapiensMutation(s): 0 
Gene Names: SAMHD1 (MOP5)
EC: 3.1.5.-
Find proteins for Q9Y3Z3 (Homo sapiens)
Go to Gene View: SAMHD1
Go to UniProtKB:  Q9Y3Z3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, C, D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.545α = 90.00
b = 80.817β = 114.93
c = 147.665γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Data collection