5A7R

Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Synthesis of Dimeric Adp-Ribose and its Structure with Human Poly(Adp-Ribose) Glycohydrolase.

Lambrecht, M.J.Brichacek, M.Barkauskaite, E.Ariza, A.Ahel, I.Hergenrother, P.J.

(2015) J Am Chem Soc 137: 3558

  • DOI: 10.1021/ja512528p
  • Primary Citation of Related Structures:  
    5A7R

  • PubMed Abstract: 
  • Poly(ADP-ribosyl)ation is a common post-translational modification that mediates a wide variety of cellular processes including DNA damage repair, chromatin regulation, transcription, and apoptosis. The difficulty associated with accessing poly(ADP-ribose) (PAR) in a homogeneous form has been an impediment to understanding the interactions of PAR with poly(ADP-ribose) glycohydrolase (PARG) and other binding proteins ...

    Poly(ADP-ribosyl)ation is a common post-translational modification that mediates a wide variety of cellular processes including DNA damage repair, chromatin regulation, transcription, and apoptosis. The difficulty associated with accessing poly(ADP-ribose) (PAR) in a homogeneous form has been an impediment to understanding the interactions of PAR with poly(ADP-ribose) glycohydrolase (PARG) and other binding proteins. Here we describe the chemical synthesis of the ADP-ribose dimer, and we use this compound to obtain the first human PARG substrate-enzyme cocrystal structure. Chemical synthesis of PAR is an attractive alternative to traditional enzymatic synthesis and fractionation, allowing access to products such as dimeric ADP-ribose, which has been detected but never isolated from natural sources. Additionally, we describe the synthesis of an alkynylated dimer and demonstrate that this compound can be used to synthesize PAR probes including biotin and fluorophore-labeled compounds. The fluorescently labeled ADP-ribose dimer was then utilized in a general fluorescence polarization-based PAR-protein binding assay. Finally, we use intermediates of our synthesis to access various PAR fragments, and evaluation of these compounds as substrates for PARG reveals the minimal features for substrate recognition and enzymatic cleavage. Homogeneous PAR oligomers and unnatural variants produced from chemical synthesis will allow for further detailed structural and biochemical studies on the interaction of PAR with its many protein binding partners.


    Organizational Affiliation

    †Department of Chemistry, Roger Adams Laboratory, University of Illinois, 600 South Mathews, Urbana, Illinois 61801, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLY(ADP-RIBOSE) GLYCOHYDROLASEA531Homo sapiensMutation(s): 7 
Gene Names: PARG
EC: 3.2.1.143
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W56 (Homo sapiens)
Explore Q86W56 
Go to UniProtKB:  Q86W56
PHAROS:  Q86W56
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
B [auth A], C [auth A][(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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A] , M [auth A] , N [auth A] , O [auth A] , P [auth A] , Q [auth A] , R [auth A] , S [auth A] , 
L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
D [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
PPI
Query on PPI

Download Ideal Coordinates CCD File 
AA [auth A], BA [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.457α = 90
b = 91.277β = 90
c = 96.123γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release