PDBsum entry 4yxw

Hydrolase

PDB id: 4yxw

Contents

Protein chains

489 a.a.

467 a.a.

213 a.a.

128 a.a.

47 a.a.

Ligands

ANP ×5

TS6

Metals

_MG ×5

_CL

_NA

Waters ×37

PDB id:

4yxw

Name:

Hydrolase

Title:

Bovine heart mitochondrial f1-atpase inhibited by amp-pnp and adp 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. Atp synthase subunit delta, mitochondrial. Chain: h.

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Tissue: muscle

Resolution:

3.10Å R-factor: 0.229 R-free: 0.273

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:

23-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: 489 a.a.*

Protein chains

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

Seq: 528 a.a.

Struc: 467 a.a.

Protein chain

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

Seq: 298 a.a.

Struc: 213 a.a.

Protein chain

P05630  (ATPD_BOVIN) -  ATP synthase subunit delta, mitochondrial from Bos taurus

Seq: 168 a.a.

Struc: 128 a.a.

Protein chain

P05632  (ATP5E_BOVIN) -  ATP synthase subunit epsilon, mitochondrial from Bos taurus

Seq: 51 a.a.

Struc: 47 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: 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 + H2O + 4 × H(+)(in) = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + 5 × H(+)(out) (Bound ligand (Het Group name = TS6) matches with 66.67% similarity)

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°.