5ZE9

Crystal structure of AMP-PNP bound mutant A3B3 complex from Enterococcus hirae V-ATPase

Summary for 5ZE9

• Entry DOI: 10.2210/pdb5ze9/pdb
• Descriptor: V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (7 entities in total)
• Functional Keywords: p-loop, hydrolase
• Biological source: Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258); More
• Total number of polymer chains: 6
• Total formula weight: 359734.54

Authors

Maruyama, S.,Suzuki, K.,Sasaki, H.,Mizutani, K.,Saito, Y.,Imai, F.L.,Ishizuka-Katsura, Y.,Shirouzu, M.,Ichiro, Y.,Murata, T. (deposition date: 2018-02-27, release date: 2019-02-06, Last modification date: 2023-11-22)

Primary citation

Maruyama, S.,Suzuki, K.,Imamura, M.,Sasaki, H.,Matsunami, H.,Mizutani, K.,Saito, Y.,Imai, F.L.,Ishizuka-Katsura, Y.,Kimura-Someya, T.,Shirouzu, M.,Uchihashi, T.,Ando, T.,Yamato, I.,Murata, T.
Metastable asymmetrical structure of a shaftless V1motor.
Sci Adv, 5:eaau8149-eaau8149, 2019

PubMed Abstract: V-ATPase is an ATP-driven rotary motor that is composed of a ring-shaped AB complex and a central DF shaft. The nucleotide-free AB complex of , composed of three identical AB heterodimers, showed a unique asymmetrical structure, probably due to the strong binding of the N-terminal barrel domain, which forms a crown structure. Here, we mutated the barrel region to weaken the crown, and performed structural analyses using high-speed atomic force microscopy and x-ray crystallography of the mutant AB. The nucleotide-free mutant AB complex had a more symmetrical open structure than the wild type. Binding of nucleotides produced a closely packed spiral-like structure with a disrupted crown. These findings suggest that wild-type AB forms a metastable (stressed) asymmetric structure composed of unstable AB conformers due to the strong constraint of the crown. The results further the understanding of the principle of the cooperative transition mechanism of rotary motors.

PubMed: 30729160
DOI: 10.1126/sciadv.aau8149

Experimental method

X-RAY DIFFRACTION (2.102 Å)