8RSK | pdb_00008rsk

Crystal structure of Methanobrevibacter oralis macrodomain in complex with Asn-ADPr

  • Classification: HYDROLASE
  • Organism(s): Methanobrevibacter oralis
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-01-24 Released: 2024-09-25 
  • Deposition Author(s): Ariza, A.
  • Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.220 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RSK

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains.

Ariza, A.Liu, Q.Cowieson, N.P.Ahel, I.Filippov, D.V.Rack, J.G.M.

(2024) J Biological Chem 300: 107770-107770

  • DOI: https://doi.org/10.1016/j.jbc.2024.107770
  • Primary Citation Related Structures: 
    8RSI, 8RSJ, 8RSK, 8RSL, 8RSM, 8RSN

  • PubMed Abstract: 

    Dynamic ADP-ribosylation signalling is a crucial pathway that controls fundamental cellular processes, in particular, the response to cellular stresses such as DNA damage, reactive oxygen species and infection. In some pathogenic microbes the response to oxidative stress is controlled by a SirTM/zinc-containing macrodomain (Zn-Macro) pair responsible for establishment and removal of the modification, respectively. Targeting this defence mechanism against the host's innate immune response may lead to novel approaches to support the fight against emerging antimicrobial resistance. Earlier studies suggested that Zn-Macros play a key role in the activation of this defence. Therefore, we used phylogenetic, biochemical, and structural approaches to elucidate the functional properties of these enzymes. Using the substrate mimetic asparagine-ADP-ribose as well as the ADP-ribose product, we characterise the catalytic role of the zinc ion in the removal of the ADP-ribosyl modification. Furthermore, we determined structural properties that contribute to substrate selectivity within the different Zn-Macro branches. Together, our data not only give new insights into the Zn-Macro family but also highlight their distinct features that may be exploited for the development of future therapies.


  • Organizational Affiliation
    • School of Biosciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.

Macromolecule Content 

  • Total Structure Weight: 92.29 kDa 
  • Atom Count: 6,647 
  • Modeled Residue Count: 786 
  • Deposited Residue Count: 786 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-acetyl-ADP-ribose deacetylase
A, B, C
262Methanobrevibacter oralisMutation(s): 0 
Gene Names: ymdBMBORA_13990
EC: 3.5.1 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for A0A166ACJ5 (Methanobrevibacter oralis)
Explore A0A166ACJ5 
Go to UniProtKB:  A0A166ACJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A166ACJ5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H20
(Subject of Investigation/LOI)

Query on A1H20



Download:Ideal Coordinates CCD File
F [auth A],
O [auth B],
S [auth C]
(2~{S})-4-[[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]amino]-2-azanyl-4-oxidanylidene-butanoic acid
C19 H29 N7 O16 P2
IIHQVAIQZCEYCA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
P [auth B]
T [auth C]
U [auth C]
H [auth A],
I [auth A],
P [auth B],
T [auth C],
U [auth C],
V [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
G [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
J [auth A],
W [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.146α = 90
b = 110.443β = 119.559
c = 104.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-09-25 
  • Deposition Author(s): Ariza, A.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210634
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R007195/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W016613/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/X007472/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Database references, Structure summary