3VR6

Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]

Summary for 3VR6

• Entry DOI: 10.2210/pdb3vr6/pdb
• Related: 3VR2 3VR3 3VR4 3VR5
• Descriptor: V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B, V-type sodium ATPase subunit D, ... (7 entities in total)
• Functional Keywords: v-atpase, enterococcus hirae, rotary motor, p-loop, hydrolase, na(+)-atpase, atp binding
• Biological source: Enterococcus hirae; More
• Total number of polymer chains: 8
• Total formula weight: 393075.47

Authors

Arai, S.,Saijo, S.,Suzuki, K.,Mizutani, K.,Kakinuma, Y.,Ishizuka-Katsura, Y.,Ohsawa, N.,Terada, T.,Shirouzu, M.,Yokoyama, S.,Iwata, S.,Yamato, I.,Murata, T. (deposition date: 2012-04-03, release date: 2013-01-16, Last modification date: 2023-11-08)

Primary citation

Arai, S.,Saijo, S.,Suzuki, K.,Mizutani, K.,Kakinuma, Y.,Ishizuka-Katsura, Y.,Ohsawa, N.,Terada, T.,Shirouzu, M.,Yokoyama, S.,Iwata, S.,Yamato, I.,Murata, T.
Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493:703-707, 2013

PubMed Abstract: In various cellular membrane systems, vacuolar ATPases (V-ATPases) function as proton pumps, which are involved in many processes such as bone resorption and cancer metastasis, and these membrane proteins represent attractive drug targets for osteoporosis and cancer. The hydrophilic V(1) portion is known as a rotary motor, in which a central axis DF complex rotates inside a hexagonally arranged catalytic A(3)B(3) complex using ATP hydrolysis energy, but the molecular mechanism is not well defined owing to a lack of high-resolution structural information. We previously reported on the in vitro expression, purification and reconstitution of Enterococcus hirae V(1)-ATPase from the A(3)B(3) and DF complexes. Here we report the asymmetric structures of the nucleotide-free (2.8 Å) and nucleotide-bound (3.4 Å) A(3)B(3) complex that demonstrate conformational changes induced by nucleotide binding, suggesting a binding order in the right-handed rotational orientation in a cooperative manner. The crystal structures of the nucleotide-free (2.2 Å) and nucleotide-bound (2.7 Å) V(1)-ATPase are also reported. The more tightly packed nucleotide-binding site seems to be induced by DF binding, and ATP hydrolysis seems to be stimulated by the approach of a conserved arginine residue. To our knowledge, these asymmetric structures represent the first high-resolution view of the rotational mechanism of V(1)-ATPase.

PubMed: 23334411
DOI: 10.1038/nature11778

Experimental method

X-RAY DIFFRACTION (2.68 Å)