PDBsum entry 5hkk

Hydrolase

PDB id: 5hkk

Contents

Protein chains

(+ 0 more) 475 a.a.

(+ 0 more) 461 a.a.

284 a.a.

132 a.a.

Ligands

ADP ×12

GOL

PO4 ×2

ATP ×2

Metals

_MG ×12

Waters ×286

PDB id:

5hkk

Name:

Hydrolase

Title:

Caldalaklibacillus thermarum f1-atpase (wild type)

Structure:

Atp synthase subunit alpha. Chain: a, b, c, i, j, k. Synonym: atp synthase f1 sector subunit alpha,f-atpase subunit alpha. Engineered: yes. Atp synthase subunit beta. Chain: d, e, f, l, m, n. Synonym: atp synthase f1 sector subunit beta,f-atpase subunit beta. Engineered: yes. Atp synthase gamma chain.

Source:

Caldalkalibacillus thermarum ta2.A1. Organism_taxid: 986075. Gene: atpa, cathta2_2809. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: c41. Gene: atpd, cathta2_2807. Gene: atpg, cathta2_2808. Gene: atpc, cathta2_2806.

Resolution:

3.00Å R-factor: 0.205 R-free: 0.246

Authors:

S.A.Ferguson,G.M.Cook,M.G.Montgomery,A.G.W.Leslie,J.E.Walker

Key ref:

S.A.Ferguson et al. (2016). Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum. Proc Natl Acad Sci U S A, 113, 10860-10865. PubMed id: 27621435 DOI: 10.1073/pnas.1612035113

Date:

14-Jan-16 Release date: 21-Sep-16

Protein chains

F5LA74  (F5LA74_9BACI) -  ATP synthase subunit alpha from Caldalkalibacillus thermarum (strain TA2.A1)

Seq: 505 a.a.

Struc: 475 a.a.

Protein chains

F5LA72  (F5LA72_9BACI) -  ATP synthase subunit beta from Caldalkalibacillus thermarum (strain TA2.A1)

Seq: 462 a.a.

Struc: 461 a.a.

Protein chains

F5LA73  (F5LA73_9BACI) -  ATP synthase gamma chain from Caldalkalibacillus thermarum (strain TA2.A1)

Seq: 286 a.a.

Struc: 284 a.a.

Protein chains

F5LA71  (F5LA71_9BACI) -  ATP synthase epsilon chain from Caldalkalibacillus thermarum (strain TA2.A1)

Seq: 135 a.a.

Struc: 132 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, I, J, K, L, M, N: 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 (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + 5 × H(+)(out) (Bound ligand (Het Group name = PO4) corresponds exactly)

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

reference

DOI no: 10.1073/pnas.1612035113

Proc Natl Acad Sci U S A 113:10860-10865 (2016)

PubMed id: 27621435

Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.

S.A.Ferguson, G.M.Cook, M.G.Montgomery, A.G.Leslie, J.E.Walker.

ABSTRACT

The crystal structure has been determined of the F1-catalytic domain of the F-ATPase from Caldalkalibacillus thermarum, which hydrolyzes adenosine triphosphate (ATP) poorly. It is very similar to those of active mitochondrial and bacterial F1-ATPases. In the F-ATPase from Geobacillus stearothermophilus, conformational changes in the ε-subunit are influenced by intracellular ATP concentration and membrane potential. When ATP is plentiful, the ε-subunit assumes a "down" state, with an ATP molecule bound to its two C-terminal α-helices; when ATP is scarce, the α-helices are proposed to inhibit ATP hydrolysis by assuming an "up" state, where the α-helices, devoid of ATP, enter the α3β3-catalytic region. However, in the Escherichia coli enzyme, there is no evidence that such ATP binding to the ε-subunit is mechanistically important for modulating the enzyme's hydrolytic activity. In the structure of the F1-ATPase from C. thermarum, ATP and a magnesium ion are bound to the α-helices in the down state. In a form with a mutated ε-subunit unable to bind ATP, the enzyme remains inactive and the ε-subunit is down. Therefore, neither the γ-subunit nor the regulatory ATP bound to the ε-subunit is involved in the inhibitory mechanism of this particular enzyme. The structure of the α3β3-catalytic domain is likewise closely similar to those of active F1-ATPases. However, although the βE-catalytic site is in the usual "open" conformation, it is occupied by the unique combination of an ADP molecule with no magnesium ion and a phosphate ion. These bound hydrolytic products are likely to be the basis of inhibition of ATP hydrolysis.