A-ATP Synthase

Introduction

The A1Ao ATP synthase derived from archaea represents a class of chimeric ATPases/synthase , whose function and general structural design share characteristics both with vacuolar V1V0 ATPases and with F1Fo ATP synthases ^[1]. A1A0 ATP synthase catalyzes the formation of the energy currency ATP by a membrane-embedded electrically-driven motor. The archaeon in this study, Pyrococcus horikoshii OT3 is an anaerobic thermophile residing in oceanic deep sea vents with an optimal growth temperature of 100degrees. Anaerobic fermentation is its principle metabolic pathway. The specific enzymatic process in A-ATP synthase reveals novel, exceptional subunit composition and coupling stoichiometries that may reflect the differences in energy-conserving mechanisms as well as adaptation to temperatures at or above 100 degrees C. Because some archaea are rooted close to the origin in the tree of life, these unusual mechanisms are considered to have developed very early in the history of life and, therefore, may represent the first energy-conserving mechanisms. ^[2]

Structure

A-ATP synthase is composed of two parts A1"' and A0 composed of at least nine subunits A3B3C:D:E:F:H2:a:cx that function as a pair of rotary motors connected by central and peripheral stalk(s) ^[2].The A0 domain is the hydrophobic membrane embedded ion-translocating sector that uses the H+ gradient to power ATP synthase in domain A1. A1 is catalytic and water soluble containing A and B subunits. These subunits are comparable to F-ATP synthase ATP synthase alpha/beta subunits. ATPsyn.gif The A subunit of A1 is catalytic and the B subunit is regulatory, with a substrate-binding site on each.

Within the catalytic A subunit there are four domains, the N-terminal residues 1-79, 110-116, 189-199, non-homologous residues 117-188, nucleotide binding alpha-beta residues 80-99, 200-437, and C-terminal alpha helical bundle residues 438-588 domains. figure1.

The P-Loop is the eight residue consensus sequence GPFGSGKT 234-241. The P-loop or phosphate binding loop is conserved only within the A subunits and is a glycine-rich loop preceded by a beta sheet and followed by an alpha helix. It interacts with the phosphate groups of the nucleotide and with a magnesium ion at residue K240 and T241 , which coordinates the β- and γ-phosphates. This P-loop has an arched conformation unique to A-ATP Synthase, indicating that the mode of nucleotide binding and the catalytic mechanism is different from that of other syntheses. ^[3] For example, in A-ATP Synthases F236 is involved in P-Loop stabilization, but its equivalent (alanine) in subunit B of the F-ATP syntheses subunit beta is a key residue in the catalytic process in moving towards the y-phosphate of ATP during catalysis.

Transition State Stabilization

Five steps inside the catalytic A-subunit are critical for catalysis. Substrate entrance, phosphate and nucleotide binding, transition-state formation, ATP formation, and product release. The vanadate bound model mimics the transition state. Orthovandate is a transition state analog useful because it can adapt both tetragonal and trigonal bipyramidal coordination geometry. Fig. 1. The Avi structure can be compared to the As sulfate bound structure and the Apnp AMP-PNP bound structure. As is analogous to the phosphate binding (substrate) structure and Apnp is analogous to the ATP binding (product) structure^[4]. A reaction coordination is generated from freeze frame picture of reactants such as "'As"' "'Avi"' and "Apnp". The movement of specific residues to stabilize the transition state is demonstrated by comparing the deviations between the three structures. pic Although not at bonding distances the residues K240 R264 E263 move closer to the vanadate with respect to the two other structures and are proposed to stabilize the transition state during catalysis.

Residue S238 is polar and 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.

In "'F-ATP Synthase"' the homolog to S238 is the non polar A158. Since A158 cannot form hydrogen bonds to interact with the substrate, the P-loop undergoes a conformational change. In A-ATP Synthase the close proximity needed between S238 and the vandate during transition state is achieved with a hydrogen bond, not a conformational change in the P-loop.

By comparing the average distances of the alpha carbons of the P-loop residues to the sulfate, vanadate, and PNP molecules, it was found that the PNP molecule is closest, followed by the vanadate then the sulfate. grah

[[The r.m.s.d from As to Avi is 1.18 angstroms. On average the P-loop residues a-carbon (234-241) are closer to the vandate molecule than to the sulfonate molecule, by 1.25 angstroms. The r.m.s.d from Avi to Apnp is 1.04 angstroms. P-loop residues are located at increasingly greater distances from the y-phosphate of AMP-PNP versus vandate versus sulfate, which shows that vanadate occupies an intermediate position.]]

ger loop is placed above the p loop. 262-277 page 742. IS proposed to be important for catalytic function. Proposed to be involved in the immobilization and polarization of a water molecule to facilitate nucleophilic attack at the y-phosphate of ATP.

R349-

also stabilized by weak non-polar interactions and polar. K162+ R189+ E188-

These increased proximities of the catalytically important residues clearly demonstrate that structural rearrangement occurs during catalysis in subunit A.

^[5]

Significance of the Second Vandate

The second vandate is positioned in a region exactly opposite the nucleotide-binding site, where the ATP molecule transiently associates on its way to the final binding pocket in subunit "'B"'. [25] L417 Is involved in a bifurcated hydrogen bond with the second vandate. Similar binding behavior was observed for "'As"' [10] indicating that the substrate molecule has a similar path of entry to the active site in both the "'A"' and '"B"' subunit of the A-ATP synthase and that they have a transient binding position near the P-Loop. It is proposed that Pi binds first to the catalytic site and sterically hinders ATP binding, thereby selectively allowing binding of ADP [14] The "'Avi"' structure confirms this, since although both ADP and Vi were present in the crystallized solution, the catalytic A-subunit first permits only the binding of the phosphate analogue Vi. Hence the present "Avi"' structure represents a trapped initial transition state showing for the first time both the entering path and the final Vi-bound state in the catalytic subunit.

Conclusion

The active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side chains which make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. Stabilization of the transition state supports the induced fit model. A-ATP synthase lowers the activation energy by creating an environment in which the transition state is stabilized

(e.g. straining the shape of a substrate—by binding the transition-state conformation of the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition state form, thereby reducing the amount of energy required to complete the transition).

when the enzyme is complementary to the substrate, the E.S. complex is more stable, has less free energy in the ground state than substrate alone. This increases the activation energy.

Pi binds before ADP. is synthase reversible? where is it located? absence of ADP, may not affect the formation of transition-like state because of example