8W14 | pdb_00008w14

Rhodanese-like domain from Acinetobacter baumannii 118362


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Literature

Structural and biochemical characterization of an encapsulin-associated rhodanese from Acinetobacter baumannii.

Benisch, R.Giessen, T.W.

(2024) Protein Sci 33: e5129-e5129

  • DOI: https://doi.org/10.1002/pro.5129
  • Primary Citation Related Structures: 
    8W14

  • PubMed Abstract: 

    Rhodanese-like domains (RLDs) represent a widespread protein family canonically involved in sulfur transfer reactions between diverse donor and acceptor molecules. RLDs mediate these transsulfuration reactions via a transient persulfide intermediate, created by modifying a conserved cysteine residue in their active sites. RLDs are involved in various aspects of sulfur metabolism, including sulfide oxidation in mitochondria, iron-sulfur cluster biogenesis, and thio-cofactor biosynthesis. However, due to the inherent complexity of sulfur metabolism caused by the intrinsically high nucleophilicity and redox sensitivity of thiol-containing compounds, the physiological functions of many RLDs remain to be explored. Here, we focus on a single domain Acinetobacter baumannii RLD (Ab-RLD) associated with a desulfurase encapsulin which is able to store substantial amounts of sulfur inside its protein shell. We determine the 1.6 Å x-ray crystal structure of Ab-RLD, highlighting a homodimeric structure with a number of unusual features. We show through kinetic analysis that Ab-RLD exhibits thiosulfate sulfurtransferase activity with both cyanide and glutathione acceptors. Using native mass spectrometry and in vitro assays, we provide evidence that Ab-RLD can stably carry a persulfide and thiosulfate modification and may employ a ternary catalytic mechanism. Our results will inform future studies aimed at investigating the functional link between Ab-RLD and the desulfurase encapsulin.


  • Organizational Affiliation
    • Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA.

Macromolecule Content 

  • Total Structure Weight: 38.7 kDa 
  • Atom Count: 2,781 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 342 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhodanese
A, B
171Acinetobacter baumannii 118362Mutation(s): 0 
EC: 2.8.1.1
UniProt
Find proteins for A0A654L513 (Acinetobacter baumannii (strain MDR-ZJ06))
Explore A0A654L513 
Go to UniProtKB:  A0A654L513
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A654L513
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.74α = 90
b = 69.74β = 90
c = 133.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133325

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release