PDBsum entry 2dpy

Hydrolase

PDB id: 2dpy

Contents

Protein chains

422 a.a. *

Ligands

ADP

Waters ×133

* Residue conservation analysis

PDB id:

2dpy

Name:

Hydrolase

Title:

Crystal structure of the flagellar type iii atpase flii

Structure:

Flagellum-specific atp synthase. Chain: a, b. Fragment: residues 19-456. Synonym: flii. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.244 R-free: 0.295

Authors:

K.Imada,K.Namba,T.Minamino

Key ref:

K.Imada et al. (2007). Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits. Proc Natl Acad Sci U S A, 104, 485-490. PubMed id: 17202259 DOI: 10.1073/pnas.0608090104

Date:

18-May-06 Release date: 26-Dec-06

Protein chains

P26465  (FLII_SALTY) -  Flagellum-specific ATP synthase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 456 a.a.

Struc: 422 a.a.

Enzyme reactions

• Enzyme class: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

ATP + H2O + 4 × H(+)(in) = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + 5 × H(+)(out)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0608090104

Proc Natl Acad Sci U S A 104:485-490 (2007)

PubMed id: 17202259

Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits.

K.Imada, T.Minamino, A.Tahara, K.Namba.

ABSTRACT

Construction of the bacterial flagellum in the cell exterior proceeds at its distal end by highly ordered self-assembly of many different component proteins, which are selectively exported through the central channel of the growing flagellum by the flagellar type III export apparatus. FliI is the ATPase of the export apparatus that drives the export process. Here we report the 2.4 A resolution crystal structure of FliI in the ADP-bound form. FliI consists of three domains, and the whole structure shows extensive similarities to the alpha and beta subunits of F0F1-ATPsynthase, a rotary motor that drives the chemical reaction of ATP synthesis. A hexamer model of FliI has been constructed based on the F1-ATPase structure composed of the alpha3beta3gamma subunits. Although the regions that differ in conformation between FliI and the F1-alpha/beta subunits are all located on the outer surface of the hexamer ring, the main chain structures at the subunit interface and those surrounding the central channel of the ring are well conserved. These results imply an evolutionary relation between the flagellum and F0F1-ATPsynthase and a similarity in the mechanism between FliI and F1-ATPase despite the apparently different functions of these proteins.

Selected figure(s)

Figure 2.
Fig. 2. Structure of FliI( 1–18). (A) C^ ribbon drawing of FliI( 1–18). All of the secondary structure elements are labeled as in Fig. 1. The linker connecting the N-terminal and ATPase domains, which is missing in the model, is indicated by a dashed line. (B) Close-up stereoview of the nucleotide-binding site. The bound ADP is colored green, and the residues interacting with ADP are shown in cyan. Conserved residues involved in catalysis are indicated by yellow. (C–F) Comparison of the relative domain orientation. FliI( 1–18) (cyan) is superimposed onto the F[1]- subunits in various states, for which only corresponding atoms in the ATPase domain were used for fitting: (C) [E] (green), (D) [TP] (magenta), (E) [DP] (yellow) in 1BMF (21), and (F) [ADP+Pi] (red) in 1H8E (22).

Figure 3.
Fig. 3. FliI hexamer model. (A) Stereoview of the ribbon diagram. (B–D) Superposition of FliI (blue and yellow) onto the (blue green) and (orange) subunits of F[1]-ATPase [1BMF (ref. 21)]. (B) N-terminal domain. (C) ATPase domain. (D) C-terminal domain. The N and C termini of the model are labeled for one subunit in B and D, respectively. (E–H) Electrostatic surface potential of the FliI hexamer. (E) Side view of two opposite subunits. (F) End-on view from the C-terminal side. (G) End-on view of a cross-section from the C-terminal side. (H) End-on view from the N-terminal side. Black and gray arrows indicate the hydrophobic and acidic sleeves, respectively. The surface potential is color coded as blue (positive) or red (negative).

Figures were selected by an automated process.