PDBsum entry 3w3a

Hydrolase

PDB id: 3w3a

Contents

Protein chains

(+ 0 more) 577 a.a.

(+ 0 more) 457 a.a.

210 a.a.

100 a.a.

Ligands

ADP ×4

PDB id:

3w3a

Name:

Hydrolase

Title:

Crystal structure of v1-atpase at 3.9 angstrom resolution

Structure:

V-type atp synthase alpha chain. Chain: a, b, c, i, j, k. Fragment: subunit a. Synonym: v-atpase subunit a. V-type atp synthase beta chain. Chain: d, e, f, l, m, n. Fragment: subunit b. Synonym: v-atpase subunit b. V-type atp synthase subunit d.

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Strain: hb8 / atcc 27634 / dsm 579

Resolution:

3.90Å R-factor: 0.328 R-free: 0.381

Authors:

Y.Nagamatsu,K.Takeda,T.Kuranaga,N.Numoto,K.Miki

Key ref:

Y.Nagamatsu et al. (2013). Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus. J Mol Biol, 425, 2699-2708. PubMed id: 23639357 DOI: 10.1016/j.jmb.2013.04.022

Date:

14-Dec-12 Release date: 15-May-13

Protein chains

Q56403  (VATA_THET8) -  V-type ATP synthase alpha chain from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 578 a.a.

Struc: 577 a.a.

Protein chains

Q56404  (VATB_THET8) -  V-type ATP synthase beta chain from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 478 a.a.

Struc: 457 a.a.

Protein chains

O87880  (VATD_THET8) -  V-type ATP synthase subunit D from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 223 a.a.

Struc: 210 a.a.

Protein chains

P74903  (VATF_THET8) -  V-type ATP synthase subunit F from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 104 a.a.

Struc: 100 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, I, J, K: 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 = ADP) corresponds exactly) + phosphate + 5 × H(+)(out)

• Enzyme class 3: Chains D, E, F, G, H, L, M, N, O, P: E.C.3.6.3.14 - Transferred entry: 7.1.2.2.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

ATP + H(2)O + 4 × H(+)(In) = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + 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: 10.1016/j.jmb.2013.04.022

J Mol Biol 425:2699-2708 (2013)

PubMed id: 23639357

Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus.

Y.Nagamatsu, K.Takeda, T.Kuranaga, N.Numoto, K.Miki.

ABSTRACT

V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases. Here, we report a complete model of the extra-membrane domain of the V-ATPase (V1-ATPase) of a thermophilic bacterium, Thermus thermophilus, consisting of three A subunits, three B subunits, one D subunit, and one F subunit. The X-ray structure at 3.9Å resolution provides detailed information about the interactions between A3B3 and DF subcomplexes as well as interactions among the respective subunits, which are defined by the properties of side chains. Asymmetry at the intersubunit interfaces was detected from the structural differences among the three AB pairs in the different reaction states, while the large interdomain motion in the catalytic A subunits was not observed unlike F1 from various species and V1 from Enterococcus hirae. Asymmetry is mainly realized by rigid-body rearrangements of the relative position between A and B subunits. This is consistent with the previous observations by the high-resolution electron microscopy for the whole V-ATPase complexes. Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits.