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

PDB id:

4z1m

Name:

Hydrolase

Title:

Bovine f1-atpase inhibited by three copies of the inhibitor protein if1 crystallised in the presence of thiophosphate.

Structure:

Atp synthase subunit alpha, mitochondrial. Chain: a, b, c. Atp synthase subunit beta, mitochondrial. Chain: d, e, f. Atp synthase subunit gamma, mitochondrial. Chain: g. Synonym: f-atpase gamma subunit. Atpase inhibitor, mitochondrial. Chain: h, i, j.

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Gene: atpif1, atpi. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.30Å R-factor: 0.240 R-free: 0.275

Authors:

J.V.Bason,M.G.Montgomery,A.G.W.Leslie,J.E.Walker

Key ref:

J.V.Bason et al. (2015). How release of phosphate from mammalian F1-ATPase generates a rotary substep. Proc Natl Acad Sci U S A, 112, 6009-6014. PubMed id: 25918412 DOI: 10.1073/pnas.1506465112

Date:

27-Mar-15 Release date: 06-May-15

Protein chains

P19483  (ATPA_BOVIN) -  ATP synthase subunit alpha, mitochondrial from Bos taurus

Seq: 553 a.a.

Struc: 487 a.a.*

Protein chains

P00829  (ATPB_BOVIN) -  ATP synthase subunit beta, mitochondrial from Bos taurus

Seq: 528 a.a.

Struc: 469 a.a.

Protein chain

P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial from Bos taurus

Seq: 298 a.a.

Struc: 187 a.a.

Protein chain

P01096  (ATIF1_BOVIN) -  ATPase inhibitor, mitochondrial from Bos taurus

Seq: 109 a.a.

Struc: 41 a.a.*

Protein chain

P01096  (ATIF1_BOVIN) -  ATPase inhibitor, mitochondrial from Bos taurus

Seq: 109 a.a.

Struc: 28 a.a.*

Protein chain

P01096  (ATIF1_BOVIN) -  ATPase inhibitor, mitochondrial from Bos taurus

Seq: 109 a.a.

Struc: 22 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, G, H, I, J: E.C.?
• Enzyme class 3: Chains D, E, F: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O + 4 × H(+)(in) = ADP + phosphate + 5 × H(+)(out)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1506465112

Proc Natl Acad Sci U S A 112:6009-6014 (2015)

PubMed id: 25918412

How release of phosphate from mammalian F1-ATPase generates a rotary substep.

J.V.Bason, M.G.Montgomery, A.G.Leslie, J.E.Walker.

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°.