6HH3

ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-HPD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


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Literature

(ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.

Rack, J.G.M., Ariza, A., Drown, B.S., Henfrey, C., Bartlett, E., Shirai, T., Hergenrother, P.J., Ahel, I.

(2018) Cell Chem Biol 25: 1533-1546.e12

  • DOI: https://doi.org/10.1016/j.chembiol.2018.11.001
  • Primary Citation of Related Structures:  
    6G1P, 6G1Q, 6G28, 6G2A, 6HGZ, 6HH3, 6HH4, 6HH5, 6HH6, 6HOZ

  • PubMed Abstract: 

    • Protein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors ...

    Protein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors. Here we present a comprehensive structural analysis of the enzymatically active family members ARH1 and ARH3. These two enzymes have very distinct substrate requirements. Our data show that binding of the adenosine ribose moiety is highly diverged between the two enzymes, whereas the active sites harboring the distal ribose closely resemble each other. Despite this apparent similarity, we elucidate the structural basis for the selective inhibition of ARH3 by the ADP-ribose analogues ADP-HPD and arginine-ADP-ribose. Together, our biochemical and structural work provides important insights into the mode of enzyme-ligand interaction, helps to understand differences in their catalytic behavior, and provides useful tools for targeted drug design.

    Organizational Affiliation: 

    Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK. Electronic address: ivan.ahel@path.ox.ac.uk.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylhydrolase like 2
A, B
350Latimeria chalumnaeMutation(s): 0 
Gene Names: adprhl2, adprs, arh3
EC: 3.5.1 (UniProt), 3.2.1.143 (UniProt), 3.2.2 (UniProt)
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A1R
Query on A1R
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
C15 H24 N6 O12 P2
NDQDTBCXPOIQGT-UHNJQBFTSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.85α = 90
b = 98.248β = 90
c = 105.624γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2018-11-28 
    • Deposition Author(s): Ariza, A.
Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-02
    Changes: Data collection, Database references