7AQM

ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meADPr)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.

Rack, J.G.M.Liu, Q.Zorzini, V.Voorneveld, J.Ariza, A.Honarmand Ebrahimi, K.Reber, J.M.Krassnig, S.C.Ahel, D.van der Marel, G.A.Mangerich, A.McCullagh, J.S.O.Filippov, D.V.Ahel, I.

(2021) Nat Commun 12: 4581-4581

  • DOI: https://doi.org/10.1038/s41467-021-24723-3
  • Primary Citation of Related Structures:  
    7AKR, 7AKS, 7AQM, 7ARW

  • PubMed Abstract: 

    Poly(ADP-ribosyl)ation (PAR) is a versatile and complex posttranslational modification composed of repeating units of ADP-ribose arranged into linear or branched polymers. This scaffold is linked to the regulation of many of cellular processes including the DNA damage response, alteration of chromatin structure and Wnt signalling. Despite decades of research, the principles and mechanisms underlying all steps of PAR removal remain actively studied. In this work, we synthesise well-defined PAR branch point molecules and demonstrate that PARG, but not ARH3, can resolve this distinct PAR architecture. Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages. We find that ARH3-dependent hydrolysis requires both rearrangement of a catalytic glutamate and induction of an unusual, square-pyramidal magnesium coordination geometry.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylhydrolase like 2
A, B
350Latimeria chalumnaeMutation(s): 0 
Gene Names: ADPRHL2
EC: 3.5.1 (PDB Primary Data), 3.2.1.143 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt
Find proteins for H3BCW1 (Latimeria chalumnae)
Explore H3BCW1 
Go to UniProtKB:  H3BCW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH3BCW1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.825α = 90
b = 97.613β = 90
c = 107.396γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794
Wellcome TrustUnited Kingdom210634

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description