7YRY

F1-ATPase of Acinetobacter baumannii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 of Related Structures:  
    7YRY

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
514Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: atpAA1S_0153
EC: 7.1.2.2
UniProt
Find proteins for A3M142 (Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M142 
Go to UniProtKB:  A3M142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M142
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
470Acinetobacter baumannii AB5075Mutation(s): 0 
UniProt
Find proteins for A3M144 (Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M144 
Go to UniProtKB:  A3M144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M144
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainG [auth e]139Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: atpCA1S_0156
UniProt
Find proteins for A3M145 (Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M145 
Go to UniProtKB:  A3M145
Entity Groups  
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UniProt GroupA3M145
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chainH [auth g]289Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: atpGA1S_0154
UniProt
Find proteins for A3M143 (Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M143 
Go to UniProtKB:  A3M143
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M143
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
N [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
P [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
Q [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
M [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4

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: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-08-02
    Changes: Database references