3V2B

Human poly(adp-ribose) polymerase 15 (ARTD7, BAL3), macro domain 2 in complex with adenosine-5-diphosphoribose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains.

Forst, A.H., Karlberg, T., Herzog, N., Thorsell, A.G., Gross, A., Feijs, K.L., Verheugd, P., Kursula, P., Nijmeijer, B., Kremmer, E., Kleine, H., Ladurner, A.G., Schuler, H., Luscher, B.

(2013) Structure 21: 462-475

  • DOI: 10.1016/j.str.2012.12.019
  • Primary Citation of Related Structures:  
    3VFQ, 3V2B, 4D86, 4ABK, 4ABL, 3Q71, 3Q6Z

  • PubMed Abstract: 

    • ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD(+) onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, functio ...

    ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD(+) onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, function as mono-ADP-ribosyltransferases, but it has been unclear whether this modification occurs in cells and how it is read. We observed that ARTD10 colocalized with ARTD8 and defined its macrodomains 2 and 3 as readers of mono-ADP-ribosylation both in vitro and in cells. The crystal structures of these two ARTD8 macrodomains and isothermal titration calorimetry confirmed their interaction with ADP-ribose. These macrodomains recognized mono-ADP-ribosylated ARTD10, but not poly-ADP-ribosylated ARTD1. This distinguished them from the macrodomain of macroH2A1.1, which interacted with poly- but not mono-ADP-ribosylated substrates. Moreover, Ran, an ARTD10 substrate, was also read by ARTD8 macrodomains. This identifies readers of mono-ADP-ribosylated proteins, defines their structures, and demonstrates the presence of this modification in cells.

    Organizational Affiliation: 

    Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 15 A199Homo sapiensMutation(s): 0 
Gene Names: BAL3, PARP15
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for Q460N3 (Homo sapiens)
Explore Q460N3 
Go to UniProtKB:  Q460N3
NIH Common Fund Data Resources
PHAROS:  Q460N3
GTEx:  ENSG00000173200
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6
Query on AR6
Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.102α = 90
b = 91.187β = 90
c = 62.851γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references