6FOC

F1-ATPase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.331 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the catalytic domain of the ATP synthase fromMycobacterium smegmatisis a target for developing antitubercular drugs.

Zhang, A.T.Montgomery, M.G.Leslie, A.G.W.Cook, G.M.Walker, J.E.

(2019) Proc. Natl. Acad. Sci. U.S.A. --: --

  • DOI: 10.1073/pnas.1817615116

  • PubMed Abstract: 
  • The crystal structure of the F <sub>1 </sub>-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from <i>Mycobacterium smegmatis </i> which hydrolyzes ATP very poorly. The structure of the α <sub>3 </sub>β <sub>3 </sub> ...

    The crystal structure of the F 1 -catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from Mycobacterium smegmatis which hydrolyzes ATP very poorly. The structure of the α 3 β 3 -component of the catalytic domain is similar to those in active F 1 -ATPases in Escherichia coli and Geobacillus stearothermophilus However, its ε-subunit differs from those in these two active bacterial F 1 -ATPases as an ATP molecule is not bound to the two α-helices forming its C-terminal domain, probably because they are shorter than those in active enzymes and they lack an amino acid that contributes to the ATP binding site in active enzymes. In E. coli and G. stearothermophilus , the α-helices adopt an "up" state where the α-helices enter the α 3 β 3 -domain and prevent the rotor from turning. The mycobacterial F 1 -ATPase is most similar to the F 1 -ATPase from Caldalkalibacillus thermarum , which also hydrolyzes ATP poorly. The β E -subunits in both enzymes are in the usual "open" conformation but appear to be occupied uniquely by the combination of an adenosine 5'-diphosphate molecule with no magnesium ion plus phosphate. This occupation is consistent with the finding that their rotors have been arrested at the same point in their rotary catalytic cycles. These bound hydrolytic products are probably the basis of the inhibition of ATP hydrolysis. It can be envisaged that specific as yet unidentified small molecules might bind to the F 1 domain in Mycobacterium tuberculosis , prevent ATP synthesis, and inhibit the growth of the pathogen.


    Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,Department of Microbiology and Immunology, University of Otago, 9016 Dunedin, New Zealand.,The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom; walker@mrc-mbu.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha,ATP synthase subunit alpha,ATP synthase subunit alpha
A, B, C
548Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: atpA
EC: 7.1.2.2
Find proteins for A0R202 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R202
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta
D, E, F
475Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: atpD
EC: 7.1.2.2
Find proteins for A0R200 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R200
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain
G
307Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: atpG
Find proteins for A0R201 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R201
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain
H
121Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: atpC
Find proteins for A0R1Z9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R1Z9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.331 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.189α = 90.00
b = 105.189β = 90.00
c = 628.624γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105663150
Medical Research Council (United Kingdom)United KingdomMR/M009858/1
Medical Research Council (United Kingdom)United KingdomMC_U105184325
European UnionUnited Kingdom201924 EDICT

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references