PMID- 33168750 OWN - NLM STAT- MEDLINE DCOM- 20210111 LR - 20210111 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 47 DP - 2020 Nov 24 TI - The 3 x 120 degrees rotary mechanism of Paracoccus denitrificans F(1)-ATPase is different from that of the bacterial and mitochondrial F(1)-ATPases. PG - 29647-29657 LID - 10.1073/pnas.2003163117 [doi] AB - The rotation of Paracoccus denitrificans F(1)-ATPase (PdF(1)) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPgammaS), above or below K(m), PdF(1) showed three dwells per turn, each separated by 120 degrees . Analysis of dwell time between steps showed that PdF(1) executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF(1) molecules suggested that PdF(1) executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF(1) is principally a three-stepping motor similar to bacterial vacuolar (V(1))-ATPase from Thermus thermophilus This contrasts with all other known F(1)-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory zeta-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF(1) Comprehensive analysis of rotary catalysis of F(1) from different species, including PdF(1), suggests a clear trend in the correlation between the numbers of rotary steps of F(1) and F(o) domains of F-ATP synthase. F(1) motors with more distinctive steps are coupled with proton-conducting F(o) rings with fewer proteolipid subunits, giving insight into the design principle the F(1)F(o) of ATP synthase. CI - Copyright (c) 2020 the Author(s). Published by PNAS. FAU - Zarco-Zavala, Mariel AU - Zarco-Zavala M AUID- ORCID: 0000-0002-9892-0758 AD - Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan; marielzarco_zavala@comunidad.unam.mx jjgartre@unam.mx hnoji@g.ecc.u-tokyo.ac.jp. FAU - Watanabe, Ryo AU - Watanabe R AD - Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan. FAU - McMillan, Duncan G G AU - McMillan DGG AUID- ORCID: 0000-0001-6614-4494 AD - Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, the Netherlands. FAU - Suzuki, Toshiharu AU - Suzuki T AD - Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan. FAU - Ueno, Hiroshi AU - Ueno H AUID- ORCID: 0000-0001-5331-4335 AD - Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan. FAU - Mendoza-Hoffmann, Francisco AU - Mendoza-Hoffmann F AD - Department of Biology, Chemistry Faculty, National Autonomous University of Mexico, 04510 Mexico City, Mexico. FAU - Garcia-Trejo, Jose J AU - Garcia-Trejo JJ AD - Department of Biology, Chemistry Faculty, National Autonomous University of Mexico, 04510 Mexico City, Mexico marielzarco_zavala@comunidad.unam.mx jjgartre@unam.mx hnoji@g.ecc.u-tokyo.ac.jp. FAU - Noji, Hiroyuki AU - Noji H AUID- ORCID: 0000-0002-8842-6836 AD - Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan; marielzarco_zavala@comunidad.unam.mx jjgartre@unam.mx hnoji@g.ecc.u-tokyo.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201109 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 3.6.3.14 (Proton-Translocating ATPases) SB - IM MH - Adenosine Diphosphate/metabolism MH - Adenosine Triphosphate/metabolism MH - Hydrolysis MH - Kinetics MH - Mitochondria/*metabolism MH - Paracoccus denitrificans/*metabolism MH - Proton-Translocating ATPases/*metabolism MH - Rotation MH - Thermus thermophilus/metabolism PMC - PMC7703542 OTO - NOTNLM OT - F1-ATPase OT - rotation OT - single-molecule analysis OT - zeta-subunit COIS- The authors declare no competing interest. EDAT- 2020/11/11 06:00 MHDA- 2021/01/12 06:00 PMCR- 2020/11/09 CRDT- 2020/11/10 05:39 PHST- 2020/11/11 06:00 [pubmed] PHST- 2021/01/12 06:00 [medline] PHST- 2020/11/10 05:39 [entrez] PHST- 2020/11/09 00:00 [pmc-release] AID - 2003163117 [pii] AID - 202003163 [pii] AID - 10.1073/pnas.2003163117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Nov 24;117(47):29647-29657. doi: 10.1073/pnas.2003163117. Epub 2020 Nov 9.