PDBsum entry 2e5t

Hydrolase

PDB id: 2e5t

Contents

Protein chain

46 a.a.

References listed in PDB file

Key reference

Title

Structures of the thermophilic f1-Atpase epsilon subunit suggesting ATP-Regulated arm motion of its c-Terminal domain in f1.

Authors

H.Yagi, N.Kajiwara, H.Tanaka, T.Tsukihara, Y.Kato-Yamada, M.Yoshida, H.Akutsu.

Ref.

Proc Natl Acad Sci U S A, 2007, 104, 11233-11238. [DOI no: 10.1073/pnas.0701045104]

PubMed id

17581881

Abstract

The epsilon subunit of bacterial and chloroplast F(o)F(1)-ATP synthases modulates their ATP hydrolysis activity. Here, we report the crystal structure of the ATP-bound epsilon subunit from a thermophilic Bacillus PS3 at 1.9-A resolution. The C-terminal two alpha-helices were folded into a hairpin, sitting on the beta sandwich structure, as reported for Escherichia coli. A previously undescribed ATP binding motif, I(L)DXXRA, recognizes ATP together with three arginine and one glutamate residues. The E. coli epsilon subunit binds ATP in a similar manner, as judged on NMR. We also determined solution structures of the C-terminal domain of the PS3 epsilon subunit and relaxation parameters of the whole molecule by NMR. The two helices fold into a hairpin in the presence of ATP but extend in the absence of ATP. The latter structure has more helical regions and is much more flexible than the former. These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase.

Figure 3.
Fig. 3. Solution structures of the C-terminal domain of TF[1] and their relaxation prameters. (A) Superposition of 20 structures with the lowest target function values in the presence of ATP for residues 90–131. (B and C) Those in the absence of ATP. The backbone heavy atoms are superimposed for the regions comprising residues 90–102 (B) and residues 113–117 (C). (D and E) ^15N NOE, T[1], and T[2] of TF[1] amide signals in the presence (D) and absence (E) of ATP as a function of sequence number. T[2] values with asterisks at 38 and 122 are 614 and 732 ms, respectively.

Figure 5.
Fig. 5. A model for the conversion between the up-extended and down-folded subunits in F[1]. (Upper Right) Top view (from the cytoplasmic side) of a model structure of the up-extended subunit in the [3][3] complex on the basis of the crystal structure of the MF[1] [3] [3] complex (PDB ID code 1E79, Upper Left). Only N-terminal domain of MF[1] is shown. The C-terminal domain of TF[1] is represented by blue poles (stable helices in Fig. 3 B and C) and coils (flexible helices). Only C-terminal domains of the and subunits are depicted. (Lower Right) Side view from the bottom side of the top figure. (Lower Left) Side view of the folded . The rotation of the axle is clockwise on ATP hydrolysis.