8HCD

Crystal structure of mTREX1-DNA product complex (dNMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.

Huang, K.W.Wu, C.Y.Toh, S.I.Liu, T.C.Tu, C.I.Lin, Y.H.Cheng, A.J.Kao, Y.T.Chu, J.W.Hsiao, Y.Y.

(2023) Nucleic Acids Res 51: 11927-11940

  • DOI: https://doi.org/10.1093/nar/gkad910
  • Primary Citation of Related Structures:  
    8HCC, 8HCD, 8HCE, 8HCF, 8HCG, 8HCH

  • PubMed Abstract: 

    In various autoimmune diseases, dysfunctional TREX1 (Three prime Repair Exonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2'-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2'-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.


  • Organizational Affiliation

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Three-prime repair exonuclease 1A [auth B],
B [auth C],
C [auth D],
D [auth E]
276Mus musculusMutation(s): 0 
Gene Names: Trex1
EC: 3.1.11.2
Membrane Entity: Yes 
UniProt
Find proteins for Q91XB0 (Mus musculus)
Explore Q91XB0 
Go to UniProtKB:  Q91XB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XB0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGP (Subject of Investigation/LOI)
Query on DGP

Download Ideal Coordinates CCD File 
H [auth C]2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
DCM (Subject of Investigation/LOI)
Query on DCM

Download Ideal Coordinates CCD File 
F [auth B],
K [auth D],
N [auth E]
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
Q [auth E]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth B]
G [auth B]
I [auth C]
J [auth C]
L [auth D]
E [auth B],
G [auth B],
I [auth C],
J [auth C],
L [auth D],
M [auth D],
O [auth E],
P [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.68α = 90
b = 81.284β = 103.69
c = 93.209γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 111-2636-B-A49-006

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references
  • Version 1.2: 2023-12-13
    Changes: Database references