6D3A

Structure of human ARH3 D314E bound to ADP-ribose and magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition.

Pourfarjam, Y.Ventura, J.Kurinov, I.Cho, A.Moss, J.Kim, I.K.

(2018) J Biol Chem 293: 12350-12359

  • DOI: https://doi.org/10.1074/jbc.RA118.003586
  • Primary Citation of Related Structures:  
    6D36, 6D3A

  • PubMed Abstract: 

    ADP-ribosyl-acceptor hydrolase 3 (ARH3) plays important roles in regulation of poly(ADP-ribosyl)ation, a reversible post-translational modification, and in maintenance of genomic integrity. ARH3 degrades poly(ADP-ribose) to protect cells from poly(ADP-ribose)-dependent cell death, reverses serine mono(ADP-ribosyl)ation, and hydrolyzes O -acetyl-ADP-ribose, a product of Sirtuin-catalyzed histone deacetylation. ARH3 preferentially hydrolyzes O -linkages attached to the anomeric C1″ of ADP-ribose; however, how ARH3 specifically recognizes and cleaves structurally diverse substrates remains unknown. Here, structures of full-length human ARH3 bound to ADP-ribose and Mg 2+ , coupled with computational modeling, reveal a dramatic conformational switch from closed to open states that enables specific substrate recognition. The glutamate flap, which blocks substrate entrance to Mg 2+ in the unliganded closed state, is ejected from the active site when substrate is bound. This closed-to-open transition significantly widens the substrate-binding channel and precisely positions the scissile 1″- O -linkage for cleavage while securing tightly 2″- and 3″-hydroxyls of ADP-ribose. Our collective data uncover an unprecedented structural plasticity of ARH3 that supports its specificity for the 1″- O -linkage in substrates and Mg 2+ -dependent catalysis.


  • Organizational Affiliation

    From the Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(ADP-ribose) glycohydrolase ARH3A [auth C],
B [auth D],
C [auth A],
D [auth B]
366Homo sapiensMutation(s): 1 
Gene Names: ADPRHL2ARH3
EC: 3.2.1.143 (PDB Primary Data), 3.5.1 (UniProt), 3.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX46 (Homo sapiens)
Explore Q9NX46 
Go to UniProtKB:  Q9NX46
PHAROS:  Q9NX46
GTEx:  ENSG00000116863 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX46
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6
Query on AR6

Download Ideal Coordinates CCD File 
E [auth C],
G [auth D],
I [auth A],
K [auth B]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth C],
H [auth D],
J [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.901α = 83.008
b = 72.229β = 85.733
c = 115.906γ = 72.43
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations