3DSR

ADP in transition binding site in the subunit B of the energy converter A1Ao ATP synthase

Summary for 3DSR

• Entry DOI: 10.2210/pdb3dsr/pdb
• Related: 2C61 2RKW 3B2Q
• Descriptor: V-type ATP synthase beta chain, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: hydrolase, atp synthesis, hydrogen ion transport, ion transport, transport
• Biological source: Methanosarcina mazei (Methanosarcina frisia)
• Total number of polymer chains: 2
• Total formula weight: 103536.54

Authors

Kumar, A.,Manimekalai, S.M.S.,Balakrishna, A.M.,Gruber, G. (deposition date: 2008-07-14, release date: 2009-06-16, Last modification date: 2023-11-01)

Primary citation

Kumar, A.,Manimekalai, M.S.,Gruber, G.
Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphate
Acta Crystallogr.,Sect.D, 64:1110-1115, 2008

PubMed Abstract: A1A0 ATP synthases are the major energy producers in archaea. Like the related prokaryotic and eukaryotic F1F0 ATP synthases, they are responsible for most of the synthesis of adenosine triphosphate. The catalytic events of A1A0 ATP synthases take place inside the A3B3 hexamer of the A1 domain. Recently, the crystallographic structure of the nucleotide-free subunit B of Methanosarcina mazei Gö1 A1A0 ATP synthase has been determined at 1.5 A resolution. To understand more about the nucleotide-binding mechanism, a protocol has been developed to crystallize the subunit B-ADP complex. The crystallographic structure of this complex has been solved at 2.7 A resolution. The ADP occupies a position between the essential phosphate-binding loop and amino-acid residue Phe149, which are involved in the binding of the antibiotic efrapeptin in the related F1F0 ATP synthases. This trapped ADP location is about 13 A distant from its final binding site and is therefore called the transition ADP-binding position. In the trapped ADP position the structure of subunit B adopts a different conformation, mainly in its C-terminal domain and also in the final nucleotide-binding site of the central alphabeta-domain. This atomic model provides insight into how the substrate enters into the nucleotide-binding protein and thereby into the catalytic A3B3 domain.

PubMed: 19020348
DOI: 10.1107/S090744490802790X

Experimental method

X-RAY DIFFRACTION (2.7 Å)