7vw7 | pdb_00007vw7

Crystal structure of the 2 ADP-AlF4-bound V1 complex

spinqualitylabelsall models 7vw7, resolution 3.82Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7vw7 is a 8 chain structure with sequence from Enterococcus hirae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.818Å Ligands: ADP, ALF, GOL, MG, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A1V8WY35_ENTHR Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit.[HAMAP-Rule:MF_00309] Publication Abstract from PubMed The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V(1)-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography, a new intermediate or "dwell" is identified, which enables the release of an inorganic phosphate (or P(i)) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V(1)-ATPase to be the rate-limiting step of motor action. Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations.,Shekhar M, Gupta C, Suzuki K, Chan CK, Murata T, Singharoy A ACS Cent Sci. 2022 Jul 27;8(7):915-925. doi: 10.1021/acscentsci.1c01599. Epub , 2022 Jun 14. PMID:35912346 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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