PDBsum entry 4z1m

Hydrolase

PDB id: 4z1m

Contents

Protein chains

487 a.a.

469 a.a.

187 a.a.

41 a.a.

28 a.a.

22 a.a.

Ligands

ATP ×3

GOL ×2

ADP ×2

Metals

_CL ×11

_MG ×5

Waters ×25

References listed in PDB file

Key reference

• Title: How release of phosphate from mammalian f1-Atpase generates a rotary substep.
• Authors: J.V.Bason, M.G.Montgomery, A.G.Leslie, J.E.Walker.
• Ref.: Proc Natl Acad Sci U S A, 2015, 112, 6009-6014. [DOI no: 10.1073/pnas.1506465112]
• PubMed id: 25918412

Abstract

The rotation of the central stalk of F1-ATPase is driven by energy derived from the sequential binding of an ATP molecule to its three catalytic sites and the release of the products of hydrolysis. In human F1-ATPase, each 360° rotation consists of three 120° steps composed of substeps of about 65°, 25°, and 30°, with intervening ATP binding, phosphate release, and catalytic dwells, respectively. The F1-ATPase inhibitor protein, IF1, halts the rotary cycle at the catalytic dwell. The human and bovine enzymes are essentially identical, and the structure of bovine F1-ATPase inhibited by IF1 represents the catalytic dwell state. Another structure, described here, of bovine F1-ATPase inhibited by an ATP analog and the phosphate analog, thiophosphate, represents the phosphate binding dwell. Thiophosphate is bound to a site in the αEβE-catalytic interface, whereas in F1-ATPase inhibited with IF1, the equivalent site is changed subtly and the enzyme is incapable of binding thiophosphate. These two structures provide a molecular mechanism of how phosphate release generates a rotary substep as follows. In the active enzyme, phosphate release from the βE-subunit is accompanied by a rearrangement of the structure of its binding site that prevents released phosphate from rebinding. The associated extrusion of a loop in the βE-subunit disrupts interactions in the αEβE-catalytic interface and opens it to its fullest extent. Other rearrangements disrupt interactions between the γ-subunit and the C-terminal domain of the αE-subunit. To restore most of these interactions, and to make compensatory new ones, the γ-subunit rotates through 25°-30°.