ATP SYNTHASE Bovine F1ATPase

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ATP SYNTHASE(Bovine F1-ATPase )

• By Ashley, David, and Angela

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ATP Synthase

• Enzyme
• Synthesizes ATP from ADP and inorganic phosphate
• Synthesizes various forms of energy
• Projects inward from inner mitochondrial
  membranes.
• Inhibited by the Dccd (Dicyclohexylcarbodiimide)

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Overview of Structure

• FoF1 particle resembles a mushroom
• Head is the F1 particle
• Stalk is gamma subunit of F1
• Base and roots are the Fo particle embedded in
  the membrane
• Antibiotic oligomycin inhibits the Fo unit

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Mechanism
Intermembrane space
H ions

• Occurs in the outer mitochondrion compartment,
  only when NADH is made from oxidation reactions,
  which generates a proton gradient.
• As the protons build up, a proton gradient is
  formed.
• Protons (H) enter the cell through the ATP
  synthase complex- a proton channel that allows
  re-entry of protons
• The upper part of the ATP synthase complex
  rotates when a new H enters
• ATP is synthesized by the resulting current of
  protons flowing through the membrane.

Matrix
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Organisms

• Plants
• Chloroplast thylakoid membrane
• Bacteria
• Eubacteria
• Yeast
• Animal
• Humans

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Location within organism

• In plants
• ATP synthase occurs in the chloroplast and is
  intergrated into the thylakoid membrane
• F1 sticks in the stroma, where dark reaction of
  photosynthesis and ATP synthesis take place.
• In E. coli
• Simplest known form, with 8 different subunit
  types
• In yeast
• Most complex form, with 20 different subunit
  types

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Disease caused by ATP Synthase

• Autosomal dominant polycystic kidney disease
  (ADPKD)
• Monogenic disease- a modified single gene
• The C. elegans polycystins LOV-1 and PKD-2 are
  required for male mating behaviors and are
  localized to sensory cilia.
• ATP-2 and other ATP synthase components
  colocalize with LOV-1 and PKD-2 in cilia.
• Disrupts the function of the ATP synthase or over
  expression of atp-2, which results in a male
  mating behavior defect.

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Significance of ATP synthase

• The synthesis of ATP from ATP synthase causes a
  concentration gradient.
• Concentration gradients are key components to the
  biological world.
• The potential energy from these gradients are
  often used to perform biological work.

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Application uses

• Bioremediation and biodegradation-uses
  microorganisms to clean up contaminated
  environments.
• Oil spills
• Pollutants
• If it werent for ATP synthase, ATP would not be
  stored in living
• systems like
• microorganisms

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Crystal Structure of ATP SYNTHASE

• PDB 1E79

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General features

• There are a total of 9 chains and they are all
  amino acids
• Chain A,B, C are all identical
• each has a total of 510 residues with gaps, 492
  residues w/o gap.
• (gap residues1 to18)
• Chain D
• has a total of 475 residues with gaps, 466
  residues w/o gap.
• (gap11 to 8 and gap2 200)
• Chain E and F are identical
• has a total of 474 residues with gaps, 466
  residues w/o gap.
• (gap residues 1 to 8)
• Chain G
• has total of 272 residues with gaps, 263 residue
  w/o gaps.
• (gap 1 62 to 66 and gap2 97 to 100)
• Chain H
• Has total of 145 residue with gaps, 131 w/o gaps
• (gap residues 1 to 14)
• Chain I
• Has total of 47 residue with gaps, no gaps

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CHOFAS

• Predicted number of helices 14

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GOR4

• Predicted number of helices 14

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PELE

• Predicted number of helices 14

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CHOFAS

• Predicted Strands 20

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GOR4

• Predicted strands 16

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PELE

• Predicted strands 15

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Protein Explorer

• Total number of helices (red)145
• Total number of strands (yellow)107

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Ligands

• There are a total of 13 ligands for all 9 chains,
  but Chain A has 2 ligands.

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Whats around Magnesium?
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Active sites

• Chain A was not crystallized with any inhibitors,
  but general inhibitors for the enyzme,
  Dicyclohexylcarbodiimide (DCCd) and Oligomycin.
• Chain A LYS175A, ARG373A, ARG171A, GLN172A,
  THR173A, GLY174A, LYS175A, THR176A, SER177A,
  GLU328A, PHE357A, GLN430A, and GLN432A

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Domains

• There are 2 functional, which are F0 and F1.
• F1 ATPase
• Its the central domain.
• Found in bacterial plasma membranes,
  mitochondrial inner membranes, and chloroplast
  thylakoid membranes.
• F1, is composed of alpha, beta, gamma, delta and
  epsilon subunits(3a, 3ß, ?, d, e).

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Domain F0

• F0 Domain
• Is an integral membrane
• This portion is composed of 3 subunits
• A, 2-B, and 12-C
• 12-C subuints
• They are hydrophobic
• Arranged in two circle
• Circle one the inner circle, which consist of
  amino terminal
• Circle two the outer circle, which consist of
  carboxyl terminal

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Structural Motif

• There is 1 interesting structural motifs found
  for Chain A
• PS00017 151-gt159 ATP_GTP_A PDOC00017
• The best conserved of these motifs is a
  glycine-rich region, which typically forms a
  flexible loop between a beta-strand and an
  alpha-helix. This sequence motif is generally
  referred to as the P-loop.

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Chain G Motif

• A dimerization motif GXXXG within the F0 domain
  of the membrane-spanning segment
• Alteration of this motif leads to the loss of
  subunit g and of supramolecular structures of the
  ATP synthase.
• most highly studied mode of helix-helix
  association
• is known to act as a universal scaffold for the
  assembly of two transmembrane helices

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Multiple Sequence Alignment
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MSA Information

• Legend shows the conserved and non-conserved
  regions of sequence.
• Gaps are noted by a dash mark within the
  sequence.

• There are no noted indels in the sequence.

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BOXSHADE Color-Coded Plots of Pre-Aligned
Sequences
Conserved region Identical region Similar region
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Comparisons

• Shows that there are 62.8 identical regions
  between the sequences with many similar residues
  scattered throughout.
• Only 0.03 is considered a truly conserved region
  among the five sequences

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Infer an Unrooted Phylogeny from PS Alignment
PROTPARS
100
100
(((Bacterium,Plant_Thaliana),(Purple_Sea_Urchin,1E
79_g_chain)),Asian_Rooster)
Draw Unrooted Phylogenetic Tree from Alignment
DRAWTREE
(((Asian_Rooster,1E79_G_Chain) 100,
Purple_Sea_Urchin) 100 Plant_Thaliana,Bacterium)
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Summary

• 9 chains
• 2 inhibitors
• Mushroom shaped with membrane and matrix regions
• Found in almost every organism on the earth
• Very important due synthesis of energy within the
  organisms
• Most closely related to the Asian rooster based
  on our phylogenic trees

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Questions and Comments
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References

• http//www.who.int/genomics/public/geneticdiseases
  /en/index2.html
• http//www.wisc.edu/molpharm/faculty/barr/Pub15563
  610.pdf
• http//vcell.ndsu.nodak.edu/animations/atpgradient
  /movie.htm
• http//www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/
  part2/f1fo.htm
• http//en.wikipedia.org/wiki/ImageDCC_Structure.p
  ng
• http//www.mrc-dunn.cam.ac.uk/research/atp_synthas
  e/
• http//www.nature.com/nsmb/journal/v7/n11/full/nsb
  1100_1055.html
• http//www.sp.uconn.edu/terry/images/anim/ATPmito
  .html
• http//www.life.uiuc.edu/crofts/bioph354/lect10.ht
  ml
• http//en.wikipedia.org/wiki/ATP_synthase
• http//nobelprize.org/nobel_prizes/chemistry/laure
  ates/1997/press.html
• http//nobelprize.org/nobel_prizes/chemistry/laure
  ates/1997/press.html
• http//www.ncbi.nlm.nih.gov/
• http//en.wikipedia.org/wiki/Bioremediation
• Diego M. Bustos J. Biol. Chem., Vol. 280, Issue
  32, 29004-29010, August 12, 2005.
  http//www.jbc.org/cgi/content/abstract/280/32/290
  04
• Clyde Gibbons, Martin G. Montgomery, Andrew G. W.
  Leslie  John E. Walker. The structure of the
  central stalk in bovine F1-ATPase at 2.4 Å
  resolution. Nature Structural Biology  7, 1055 -
  1061 (2000). 17 April, 2008