3B2Q

Intermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter A1Ao ATP synthase

Summary for 3B2Q

• Entry DOI: 10.2210/pdb3b2q/pdb
• Related: 2RKW
• Descriptor: V-type ATP synthase beta chain, ADENOSINE-5'-TRIPHOSPHATE, 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE, ... (5 entities in total)
• Functional Keywords: hydrolase, atp synthesis, hydrogen ion transport, ion transport, transport
• Biological source: Methanosarcina mazei
• Total number of polymer chains: 2
• Total formula weight: 104069.91

Authors

Kumar, A.,Manimekalai, M.S.S.,Balakrishna, A.M.,Hunke, C.,Gruber, G. (deposition date: 2007-10-19, release date: 2008-09-09, Last modification date: 2023-11-01)

Primary citation

Kumar, A.,Manimekalai, M.S.S.,Balakrishna, A.M.,Hunke, C.,Weigelt, S.,Sewald, N.,Gruber, G.
Spectroscopic and crystallographic studies of the mutant R416W give insight into the nucleotide binding traits of subunit B of the A1Ao ATP synthase
Proteins, 75:807-819, 2009

PubMed Abstract: A strategically placed tryptophan in position of Arg416 was used as an optical probe to monitor adenosine triphosphate and adenosine-diphosphate binding to subunit B of the A(1)A(O) adenosine triphosphate (ATP) synthase from Methanosarcina mazei Gö1. Tryptophan fluorescence and fluorescence correlation spectroscopy gave binding constants indicating a preferred binding of ATP over ADP to the protein. The X-ray crystal structure of the R416W mutant protein in the presence of ATP was solved to 2.1 A resolution, showing the substituted Trp-residue inside the predicted adenine-binding pocket. The cocrystallized ATP molecule could be trapped in a so-called transition nucleotide-binding state. The high resolution structure shows the phosphate residues of the ATP near the P-loop region (S150-E158) and its adenine ring forms pi-pi interaction with Phe149. This transition binding position of ATP could be confirmed by tryptophan emission spectra using the subunit B mutant F149W. The trapped ATP position, similar to the one of the binding region of the antibiotic efrapeptin in F(1)F(O) ATP synthases, is discussed in light of a transition nucleotide-binding state of ATP while on its way to the final binding pocket. Finally, the inhibitory effect of efrapeptin C in ATPase activity of a reconstituted A(3)B(3)- and A(3)B(R416W)(3)-subcomplex, composed of subunit A and the B subunit mutant R416W, of the A(1)A(O) ATP synthase is shown.

PubMed: 19003877
DOI: 10.1002/prot.22289

Experimental method

X-RAY DIFFRACTION (2.1 Å)