5FUD

Oceanobacillus iheyensis macrodomain with MES bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional analysis ofOceanobacillus iheyensismacrodomain reveals a network of waters involved in substrate binding and catalysis.

Zapata-Perez, R.Gil-Ortiz, F.Martinez-Monino, A.B.Garcia-Saura, A.G.Juanhuix, J.Sanchez-Ferrer, A.

(2017) Open Biol 7

  • DOI: https://doi.org/10.1098/rsob.160327
  • Primary Citation of Related Structures:  
    5FUD, 5L9K, 5L9Q, 5LAU, 5LBP, 5LCC

  • PubMed Abstract: 

    Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis. The crystal structures of D40A, N30A and G37V mutants, and those with MES, ADPr and ADP bound, allowed us to identify five fixed water molecules that play a significant role in substrate binding. Closure of the β6-α4 loop is revealed as essential not only for pyrophosphate recognition, but also for distal ribose orientation. In addition, a novel structural role for residue D40 is identified. Furthermore, it is revealed that OiMacroD not only catalyses the hydrolysis of O -acetyl-ADP-ribose but also reverses protein mono-ADP-ribosylation. Finally, mutant G37V supports the participation of a substrate-coordinated water molecule in catalysis that helps to select the proper substrate conformation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus Espinardo, 30100 Murcia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-ACETYL-ADP-RIBOSE DEACETYLASE
A, B
208Oceanobacillus iheyensis HTE831Mutation(s): 0 
EC: 3.2.2 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt
Find proteins for Q8EP31 (Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831))
Explore Q8EP31 
Go to UniProtKB:  Q8EP31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EP31
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.99α = 90
b = 96.74β = 115.65
c = 54.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description