3OFN

Structure of four mutant forms of yeast F1 ATPase: alpha-N67I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Literature

Crystal structures of mutant forms of the yeast f1 ATPase reveal two modes of uncoupling.

Arsenieva, D.Symersky, J.Wang, Y.Pagadala, V.Mueller, D.M.

(2010) J Biol Chem 285: 36561-36569

  • DOI: 10.1074/jbc.M110.174383
  • Primary Citation of Related Structures:  
    3OE7, 3OEH, 3OFN

  • PubMed Abstract: 
  • The mitochondrial ATP synthase couples the flow of protons with the phosphorylation of ADP. A class of mutations, the mitochondrial genome integrity (mgi) mutations, has been shown to uncouple this process in the yeast mitochondrial ATP synthase. Four mutant forms of the yeast F(1) ATPase with mgi mutations were crystallized; the structures were solved and analyzed ...

    The mitochondrial ATP synthase couples the flow of protons with the phosphorylation of ADP. A class of mutations, the mitochondrial genome integrity (mgi) mutations, has been shown to uncouple this process in the yeast mitochondrial ATP synthase. Four mutant forms of the yeast F(1) ATPase with mgi mutations were crystallized; the structures were solved and analyzed. The analysis identifies two mechanisms of structural uncoupling: one in which the empty catalytic site is altered and in doing so, apparently disrupts substrate (phosphate) binding, and a second where the steric hindrance predicted between γLeu83 and β(DP) residues, Leu-391 and Glu-395, located in Catch 2 region, is reduced allowing rotation of the γ-subunit with less impedance. Overall, the structures provide key insights into the critical interactions in the yeast ATP synthase involved in the coupling process.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C, J, K, L, S, T, U
A, B, C, J, K, L, S, T, U
510Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: ATP1YBL0827YBL099W
EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07251
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F, M, N, O, V, W, X
D, E, F, M, N, O, V, W, X
484Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP2J2041YJR121W
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
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UniProt GroupP00830
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gammaG, P, Y278Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP3ATP3aATP3bYBR039WYBR0408
EC: 3.6.3.14
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit deltaH, Q138Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP16D2935YD8119.03YDL004W
EC: 3.6.3.14
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit epsilonI, R61Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP15P0345YPL271W
EC: 3.6.3.14
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
BA [auth B],
BB [auth X],
DA [auth C],
FA [auth D],
HA [auth F],
BA [auth B],
BB [auth X],
DA [auth C],
FA [auth D],
HA [auth F],
JA [auth J],
LA [auth K],
NA [auth L],
PA [auth M],
RA [auth O],
TA [auth S],
VA [auth T],
XA [auth U],
Z [auth A],
ZA [auth V]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth V],
CA [auth B],
CB [auth X],
EA [auth C],
AA [auth A],
AB [auth V],
CA [auth B],
CB [auth X],
EA [auth C],
GA [auth D],
IA [auth F],
KA [auth J],
MA [auth K],
OA [auth L],
QA [auth M],
SA [auth O],
UA [auth S],
WA [auth T],
YA [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.019α = 90
b = 290.619β = 102.34
c = 188.465γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance