6FOC

F1-ATPase from Mycobacterium smegmatis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.331 
  • R-Value Observed: 0.333 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 116: 4206-4211

  • DOI: 10.1073/pnas.1817615116
  • Primary Citation of Related Structures:  
    6FOC

  • PubMed Abstract: 

    • 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 ...

    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; walker@mrc-mbu.cam.ac.uk.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alpha,ATP synthase subunit alpha,ATP synthase subunit alphaA, B, C548Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpA, MSMEG_4938, MSMEI_4811
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Go to UniProtKB:  A0R202
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaD, E, F475Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpD, MSMEG_4936, MSMEI_4809
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for A0R200 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Go to UniProtKB:  A0R200
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chainG307Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpG, MSMEG_4937, MSMEI_4810
Find proteins for A0R201 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Go to UniProtKB:  A0R201
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainH121Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpC, MSMEG_4935, MSMEI_4808
Find proteins for A0R1Z9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R1Z9 
Go to UniProtKB:  A0R1Z9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download CCD File 
A, B, C, D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.331 
  • R-Value Observed: 0.333 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.189α = 90
b = 105.189β = 90
c = 628.624γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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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
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references