2BFQ

MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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This is version 1.2 of the entry. See complete history


Literature

The Macro Domain is an Adp-Ribose Binding Module.

Karras, G.I.Kustatscher, G.Buhecha, H.R.Allen, M.D.Pugieux, C.Sait, F.Bycroft, M.Ladurner, A.G.

(2005) EMBO J 24: 1911

  • DOI: 10.1038/sj.emboj.7600664
  • Primary Citation of Related Structures:  
    2BFR, 2BFQ

  • PubMed Abstract: 
  • The ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, transcription, chromatin biology and long-term memory formation. Yet no protein modules are known that specifically recognize the ADP-ribose nucleotide ...

    The ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, transcription, chromatin biology and long-term memory formation. Yet no protein modules are known that specifically recognize the ADP-ribose nucleotide. We provide biochemical and structural evidence that macro domains are high-affinity ADP-ribose binding modules. Our structural analysis reveals a conserved ligand binding pocket among the macro domain fold. Consistently, distinct human macro domains retain their ability to bind ADP-ribose. In addition, some macro domain proteins also recognize poly-ADP-ribose as a ligand. Our data suggest an important role for proteins containing macro domains in the biology of ADP-ribose.


    Organizational Affiliation

    Gene Expression Programme and Structural & Computational Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN AF1521A192Archaeoglobus fulgidusMutation(s): 0 
EC: 3.2.2
UniProt
Find proteins for O28751 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28751 
Go to UniProtKB:  O28751
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
B [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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
AL-PEPTIDE LINKINGC6 H11 N O3 SMET
Binding Affinity Annotations 
IDSourceBinding Affinity
APR PDBBind:  2BFQ Kd: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.116α = 90
b = 88.116β = 90
c = 60.28γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata 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: 2005-01-18
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy