A-ATP Synthase: Difference between revisions

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==<scene name='A-ATP_Synthase/Rotary_stalk/1'>F1 ATP Synthase Rotary Mechanism</scene>==

The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The <scene name='A-ATP_Synthase/Rotary_stalk/2'>Gamma subunit</scene> penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In ATP synthase, the central stalk interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (<scene name='A-ATP_Synthase/Rotary_stalk/8'>alpha, beta</scene> (3) domain.

The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The <scene name='A-ATP_Synthase/Rotary_stalk/12'>Gamma subunit</scene> penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In ATP synthase, the central stalk interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (<scene name='A-ATP_Synthase/Rotary_stalk/8'>alpha, beta</scene> (3) domain.

When operating as a generator, it uses the power of rotational motion to build ATP, or when operating as a motor, it breaks down ATP to spin the axle the opposite direction. The synthesis of ATP requires <scene name='A-ATP_Synthase/Rotary_stalk/4'>several steps</scene> , including the binding of ADP and phosphate, the formation of the new phosphate-phosphate bond, and release of ATP. As the axle turns, it forces the motor into three different conformations that assist these difficult steps. The beta subunits have a structural role, holding everything in place. The alpha subunits are the ATP generating parts. <ref name= Gibbons> PMID:11062563</ref>There are three catalytic nucleotide binding sites and three corresponding states induced by the central stalks rotation. In the Alternating catalytic model, the binding sites go through three different states. In the <scene name='A-ATP_Synthase/Rotary_stalk/10'>Open State</scene> ATP is released and ADP and Pi enters the active site. In the <scene name='A-ATP_Synthase/Rotary_stalk/9'>Loose state</scene> ADP and Pi are bound and the active site closes up around the molecules.The <scene name='A-ATP_Synthase/Rotary_stalk/11'>Tight State</scene> forces molecules together, catalyzing the formation of the phosphate bond.

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The <scene name='A-ATP_Synthase/3p20_main_structure/8'>P-Loop</scene>is the eight residue consensus sequence of amino acid residues 234-241 '''G'''PFGS'''GKT''' . The P-loop or phosphate binding loop is conserved only within the A subunits and is a <scene name='A-ATP_Synthase/3p20_main_structure/7'>glycine rich</scene> loop preceded by a beta sheet and followed by an alpha helix.

<scene name='A-ATP_Synthase/Vanadate_1_interactions/1'>Vanadate one</scene> occupies the ADP site. Although not at bonding distances the residues P233 G234 L417 stabilize the first vanadate in the transition state with weak nonpolar interactions. Residues K240 and T241 stabilize with polar interactions.

<scene name='A-ATP_Synthase/Vanadate_1_interactions/2'>Vanadate one</scene> occupies the ADP site. Although not at bonding distances the residues P233 G234 L417 stabilize the first vanadate in the transition state with weak nonpolar interactions. Residues K240 and T241 stabilize with polar interactions.

Residue <scene name='A-ATP_Synthase/238/5'>S238</scene> is a polar serine molecule that interacts with the nucleotides via a hydrogen bond during catalysis. The distance between residue S238 is longest in '''As''', shortest in '''Avi''' and intermediate in '''Apnp''' . In '''As''' a water molecule bridges the gap, which is removed in '''Avi'''. Dehydration of the transition state active site is reversed when ATP forms. In '''Apnp''' the water molecule interacts with the y-phosphate of ATP.

A-ATP Synthase: Difference between revisions

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@@ Line 8: / Line 8: @@
 ==<scene name='A-ATP_Synthase/Rotary_stalk/1'>F1 ATP Synthase Rotary Mechanism</scene>==
-The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The <scene name='A-ATP_Synthase/Rotary_stalk/2'>Gamma subunit</scene> penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis.  In ATP synthase, the central stalk interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (<scene name='A-ATP_Synthase/Rotary_stalk/8'>alpha, beta</scene> (3) domain.
+The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The <scene name='A-ATP_Synthase/Rotary_stalk/12'>Gamma subunit</scene> penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis.  In ATP synthase, the central stalk interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (<scene name='A-ATP_Synthase/Rotary_stalk/8'>alpha, beta</scene> (3) domain.
 When operating as a generator, it uses the power of rotational motion to build ATP, or when operating as a motor, it breaks down ATP to spin the axle the opposite direction. The synthesis of ATP requires <scene name='A-ATP_Synthase/Rotary_stalk/4'>several steps</scene> , including the binding of ADP and phosphate, the formation of the new phosphate-phosphate bond, and release of ATP. As the axle turns, it forces the motor into three different conformations that assist these difficult steps. The beta subunits have a structural role, holding everything in place. The alpha subunits are the ATP generating parts. <ref name= Gibbons> PMID:11062563</ref>There are three catalytic nucleotide binding sites and three corresponding states induced by the central stalks rotation. In the Alternating catalytic model, the binding sites go through three different states.  In the <scene name='A-ATP_Synthase/Rotary_stalk/10'>Open State</scene> ATP is released and ADP and Pi enters the active site.  In the <scene name='A-ATP_Synthase/Rotary_stalk/9'>Loose state</scene> ADP and Pi are bound and the active site closes up around the molecules.The <scene name='A-ATP_Synthase/Rotary_stalk/11'>Tight State</scene> forces molecules together, catalyzing the formation of the phosphate bond.
@@ Line 33: / Line 33: @@
 The <scene name='A-ATP_Synthase/3p20_main_structure/8'>P-Loop</scene>is the eight residue consensus sequence of amino acid residues 234-241 '''G'''PFGS'''GKT''' . The P-loop or phosphate binding loop is conserved only within the A subunits and is a <scene name='A-ATP_Synthase/3p20_main_structure/7'>glycine rich</scene> loop preceded by a beta sheet and followed by an alpha helix.
-<scene name='A-ATP_Synthase/Vanadate_1_interactions/1'>Vanadate one</scene> occupies the ADP site. Although not at bonding distances the residues P233 G234 L417 stabilize the first vanadate in the transition state with weak nonpolar interactions. Residues K240 and T241 stabilize with polar interactions.
+<scene name='A-ATP_Synthase/Vanadate_1_interactions/2'>Vanadate one</scene> occupies the ADP site. Although not at bonding distances the residues P233 G234 L417 stabilize the first vanadate in the transition state with weak nonpolar interactions. Residues K240 and T241 stabilize with polar interactions.
 Residue <scene name='A-ATP_Synthase/238/5'>S238</scene> is a polar serine molecule that interacts with the nucleotides via a hydrogen bond during catalysis. The distance between residue S238 is longest in '''As''', shortest in '''Avi''' and intermediate in '''Apnp''' . In '''As''' a water molecule bridges the gap, which is removed in '''Avi'''. Dehydration of the transition state active site is reversed when ATP forms. In '''Apnp''' the water molecule interacts with the y-phosphate of ATP.