5YIO

NMR solution structure of subunit epsilon of the Mycobacterium tuberculosis F-ATP synthase


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The NMR solution structure of Mycobacterium tuberculosis F-ATP synthase subunit epsilon provides new insight into energy coupling inside the rotary engine.

Joon, S.Ragunathan, P.Sundararaman, L.Nartey, W.Kundu, S.Manimekalai, M.S.S.Bogdanovic, N.Dick, T.Gruber, G.

(2018) FEBS J 285: 1111-1128

  • DOI: 10.1111/febs.14392
  • Primary Citation of Related Structures:  
    5YIO

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mt) F 1 F 0 ATP synthase (α 3 3 :γ:δ:ε:a:b:b':c 9 ) is essential for the viability of growing and nongrowing persister cells of the pathogen. Here, we present ...

    Mycobacterium tuberculosis (Mt) F 1 F 0 ATP synthase (α 3 3 :γ:δ:ε:a:b:b':c 9 ) is essential for the viability of growing and nongrowing persister cells of the pathogen. Here, we present the first NMR solution structure of Mtε, revealing an N-terminal β-barrel domain (NTD) and a C-terminal domain (CTD) composed of a helix-loop-helix with helix 1 and -2 being shorter compared to their counterparts in other bacteria. The C-terminal amino acids are oriented toward the NTD, forming a domain-domain interface between the NTD and CTD. The Mtε structure provides a novel mechanistic model of coupling c-ring- and ε rotation via a patch of hydrophobic residues in the NTD and residues of the CTD to the bottom of the catalytic α 3 β 3 -headpiece. To test our model, genome site-directed mutagenesis was employed to introduce amino acid changes in these two parts of the epsilon subunit. Inverted vesicle assays show that these mutations caused an increase in ATP hydrolysis activity and a reduction in ATP synthesis. The structural and enzymatic data are discussed in light of the transition mechanism of a compact and extended state of Mtε, which provides the inhibitory effects of this coupling subunit inside the rotary engine. Finally, the employment of these data with molecular docking shed light into the second binding site of the drug Bedaquiline.


    Organizational Affiliation

    Nanyang Technological University, School of Biological Sciences, Singapore, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainA121Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: atpCRv1311MTCY373.31
Find proteins for P9WPV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPV1 
Go to UniProtKB:  P9WPV1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5YIO Olderado

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Health (MOH), SingaporeSingaporeCBRG12nov049

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references, Structure summary