8HGX | pdb_00008hgx

NMR solution structure of subunit epsilon of the Acinetobacter baumannii F-ATP synthase


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Atomic insights of an up and down conformation of the Acinetobacter baumannii F 1 -ATPase subunit epsilon and deciphering the residues critical for ATP hydrolysis inhibition and ATP synthesis.

Saw, W.G.Le, K.C.M.Shin, J.Kwek, J.H.M.Wong, C.F.Ragunathan, P.Fong, T.C.Muller, V.Gruber, G.

(2023) FASEB J 37: e23040-e23040

  • DOI: https://doi.org/10.1096/fj.202300175RR
  • Primary Citation Related Structures: 
    7YRY, 8HGX

  • PubMed Abstract: 

    The Acinetobacter baumannii F 1 F O -ATP synthase (α 3 3 :γ:δ:ε:a:b 2 :c 10 ), which is essential for this strictly respiratory opportunistic human pathogen, is incapable of ATP-driven proton translocation due to its latent ATPase activity. Here, we generated and purified the first recombinant A. baumannii F 1 -ATPase (AbF 1 -ATPase) composed of subunits α 3 3 :γ:ε, showing latent ATP hydrolysis. A 3.0 Å cryo-electron microscopy structure visualizes the architecture and regulatory element of this enzyme, in which the C-terminal domain of subunit ε (Abε) is present in an extended position. An ε-free AbF 1 -ɑβγ complex generated showed a 21.5-fold ATP hydrolysis increase, demonstrating that Abε is the major regulator of AbF 1 -ATPase's latent ATP hydrolysis. The recombinant system enabled mutational studies of single amino acid substitutions within Abε or its interacting subunits β and γ, respectively, as well as C-terminal truncated mutants of Abε, providing a detailed picture of Abε's main element for the self-inhibition mechanism of ATP hydrolysis. Using a heterologous expression system, the importance of Abε's C-terminus in ATP synthesis of inverted membrane vesicles, including AbF 1 F O -ATP synthases, has been explored. In addition, we are presenting the first NMR solution structure of the compact form of Abε, revealing interaction of its N-terminal β-barrel and C-terminal ɑ-hairpin domain. A double mutant of Abε highlights critical residues for Abε's domain-domain formation which is important also for AbF 1 -ATPase's stability. Abε does not bind MgATP, which is described to regulate the up and down movements in other bacterial counterparts. The data are compared to regulatory elements of F 1 -ATPases in bacteria, chloroplasts, and mitochondria to prevent wasting of ATP.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

Macromolecule Content 

  • Total Structure Weight: 15.51 kDa 
  • Atom Count: 1,018 
  • Modeled Residue Count: 139 
  • Deposited Residue Count: 146 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain146Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VHG0 (Acinetobacter baumannii)
Explore V5VHG0 
Go to UniProtKB:  V5VHG0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VHG0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Database references