2X47

Crystal structure of human MACROD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification of Macro Domain Proteins as Novel O-Acetyl-Adp-Ribose Deacetylases.

Chen, D.Vollmar, M.Rossi, M.N.Phillips, C.Kraehenbuehl, R.Slade, D.Mehrotra, P.V.von Delft, F.Crosthwaite, S.K.Gileadi, O.Denu, J.M.Ahel, I.

(2011) J Biol Chem 286: 13261

  • DOI: 10.1074/jbc.M110.206771
  • Primary Citation of Related Structures:  
    2X47

  • PubMed Abstract: 
  • Sirtuins are a family of protein lysine deacetylases, which regulate gene silencing, metabolism, life span, and chromatin structure. Sirtuins utilize NAD(+) to deacetylate proteins, yielding O-acetyl-ADP-ribose (OAADPr) as a reaction product. The mac ...

    Sirtuins are a family of protein lysine deacetylases, which regulate gene silencing, metabolism, life span, and chromatin structure. Sirtuins utilize NAD(+) to deacetylate proteins, yielding O-acetyl-ADP-ribose (OAADPr) as a reaction product. The macrodomain is a ubiquitous protein module known to bind ADP-ribose derivatives, which diverged through evolution to support many different protein functions and pathways. The observation that some sirtuins and macrodomains are physically linked as fusion proteins or genetically coupled through the same operon, provided a clue that their functions might be connected. Indeed, here we demonstrate that the product of the sirtuin reaction OAADPr is a substrate for several related macrodomain proteins: human MacroD1, human MacroD2, Escherichia coli YmdB, and the sirtuin-linked MacroD-like protein from Staphylococcus aureus. In addition, we show that the cell extracts derived from MacroD-deficient Neurospora crassa strain exhibit a major reduction in the ability to hydrolyze OAADPr. Our data support a novel function of macrodomains as OAADPr deacetylases and potential in vivo regulators of cellular OAADPr produced by NAD(+)-dependent deacetylation.


    Organizational Affiliation

    Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53706, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MACRO DOMAIN-CONTAINING PROTEIN 1A235Homo sapiensMutation(s): 0 
Gene Names: MACROD1LRP16
EC: 3.1.1.106 (UniProt), 3.2.2 (UniProt)
Find proteins for Q9BQ69 (Homo sapiens)
Explore Q9BQ69 
Go to UniProtKB:  Q9BQ69
NIH Common Fund Data Resources
PHAROS  Q9BQ69
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.92α = 90
b = 63.41β = 90
c = 75.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references, Derived calculations, Other, Refinement description, Structure summary
  • Version 1.3: 2018-01-24
    Changes: Database references