PDBsum entry 1v9m

Hydrolase

PDB id: 1v9m

Contents

Protein chain

312 a.a. *

Ligands

GOL ×2

Waters ×165

* Residue conservation analysis

PDB id:

1v9m

Name:

Hydrolase

Title:

Crystal structure of thE C subunit of v-type atpase from thermus thermophilus

Structure:

V-type atp synthase subunit c. Chain: a. Synonym: v-type atpase subunit c, vacuolar atp synthasE C subunit. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.202 R-free: 0.228

Authors:

N.Numoto,A.Kita,K.Miki,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.Numoto et al. (2004). Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85 A resolution. Acta Crystallogr D Biol Crystallogr, 60, 810-815. PubMed id: 15103125 DOI: 10.1107/S0907444904003257

Date:

26-Jan-04 Release date: 04-May-04

Protein chain

P74902  (VATC_THET8) -  V-type ATP synthase subunit C from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 323 a.a.

Struc: 312 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.3.14 - Transferred entry: 7.1.2.2.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

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

reference

DOI no: 10.1107/S0907444904003257

Acta Crystallogr D Biol Crystallogr 60:810-815 (2004)

PubMed id: 15103125

Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85 A resolution.

N.Numoto, A.Kita, K.Miki.

ABSTRACT

The V-type H(+)-ATPases are similar to the F-type ATP synthases in their structure and functional mechanism. They hydrolyze ATP coupled with proton translocation across a membrane, but in some archaea and eubacteria they also synthesize ATP in the reverse reaction. The C subunit is one of the components of the membrane-bound V(0) moiety of V-type ATPases. The C subunit of V-type H(+)-ATPase from Thermus thermophilus was crystallized in a monoclinic form and its crystal structure was determined at 1.85 A resolution by the MAD method using selenomethionyl protein. The structure has a cone (tapered cylinder) shape consisting of only two types of helix (long and short) as secondary-structure elements. The molecule is divided into three similar domains, each of which has essentially the same topology. On the basis of the structural features and molecular-surface charge distribution, it is suggested that the bottom side of the C subunit is a possible binding site for the V(0) proteolipid L-subunit ring and that the C subunit might function as a spacer unit between the proteolipid L-subunit ring and the rotating V(1) central shaft.

Selected figure(s)

Figure 4.
Figure 4 The [A]-weighted 2F[o] - F[c] electron-density map (>1.5 ) with a superimposed ball-and-stick model of the final structure in the region containing the conserved residue Glu296. The side chain of Glu296 (H19) interacts with the main chain of Leu20 (the loop region H1-H2) with a hydrogen-bond distance of 2.71 Å. Figures were prepared with the programs MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]) and CONSCRIPT (Lawrence & Bourke, 2000[Lawrence, M. C. & Bourke, P. (2000). J. Appl. Cryst. 33, 990-991.]).

Figure 5.
Figure 5 Charge distribution of the molecular surface of the C subunit. Negatively and positively charged surfaces are coloured red and blue, respectively. (a) The bottom surface area as viewed from the opposite viewpoint to that in Fig. 1-(b). The white circle indicates the boundary between the top and bottom regions. The diameter of the circle is about 30 Å. The positively charged region spreads out of the circle indicating the binding site for the L-subunit ring, which is expected to have a negatively charged ring region (see text). (b) The top surface area as viewed from the same viewpoint as Fig. 1-(b). The figures were calculated and represented using the program GRASP (Nicholls et al., 1991[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 810-815) copyright 2004.

Figures were selected by an automated process.