7NY6

Crystal structure of the Capsaspora owczarzaki macroH2A macrodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolution of a histone variant involved in compartmental regulation of NAD metabolism.

Guberovic, I.Hurtado-Bages, S.Rivera-Casas, C.Knobloch, G.Malinverni, R.Valero, V.Leger, M.M.Garcia, J.Basquin, J.Gomez de Cedron, M.Frigole-Vivas, M.Cheema, M.S.Perez, A.Ausio, J.Ramirez de Molina, A.Salvatella, X.Ruiz-Trillo, I.Eirin-Lopez, J.M.Ladurner, A.G.Buschbeck, M.

(2021) Nat Struct Mol Biol 28: 1009-1019

  • DOI: https://doi.org/10.1038/s41594-021-00692-5
  • Primary Citation of Related Structures:  
    7NY6, 7NY7

  • PubMed Abstract: 

    NAD metabolism is essential for all forms of life. Compartmental regulation of NAD + consumption, especially between the nucleus and the mitochondria, is required for energy homeostasis. However, how compartmental regulation evolved remains unclear. In the present study, we investigated the evolution of the macrodomain-containing histone variant macroH2A1.1, an integral chromatin component that limits nuclear NAD + consumption by inhibiting poly(ADP-ribose) polymerase 1 in vertebrate cells. We found that macroH2A originated in premetazoan protists. The crystal structure of the macroH2A macrodomain from the protist Capsaspora owczarzaki allowed us to identify highly conserved principles of ligand binding and pinpoint key residue substitutions, selected for during the evolution of the vertebrate stem lineage. Metabolic characterization of the Capsaspora lifecycle suggested that the metabolic function of macroH2A was associated with nonproliferative stages. Taken together, we provide insight into the evolution of a chromatin element involved in compartmental NAD regulation, relevant for understanding its metabolism and potential therapeutic applications.


  • Organizational Affiliation

    Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute, Badalona, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone macroH2A1.1211Capsaspora owczarzaki ATCC 30864Mutation(s): 0 
Gene Names: CAOG_004778
UniProt
Find proteins for A0A0D2UG83 (Capsaspora owczarzaki (strain ATCC 30864))
Explore A0A0D2UG83 
Go to UniProtKB:  A0A0D2UG83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D2UG83
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.03α = 90
b = 44.071β = 92.36
c = 44.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-094005-B-I00
European CommissionEuropean UnionH2020-MSCA-ITN-2015-675610

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description