PDBsum entry 2j45

Nucleotide binding

PDB id: 2j45

Contents

Protein chains

297 a.a. *

Ligands

MRD ×2

MES ×3

EDO

Metals

_CA ×2

_NA

Waters ×904

* Residue conservation analysis

PDB id:

2j45

Name:

Nucleotide binding

Title:

Water structure of t. Aquaticus ffh ng domain at 1.1a resolution

Structure:

Signal recognition particle protein. Chain: a, b. Fragment: g domain, residues 1-296. Synonym: fifty-four homolog. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.14Å R-factor: 0.121 R-free: 0.154

Authors:

D.M.Freymann,U.D.Ramirez

Key ref:

U.D.Ramirez and D.M.Freymann (2006). Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh. Acta Crystallogr D Biol Crystallogr, 62, 1520-1534. PubMed id: 17139088 DOI: 10.1107/S0907444906040807

Date:

24-Aug-06 Release date: 30-Nov-06

Protein chains

O07347  (SRP54_THEAQ) -  Signal recognition particle protein from Thermus aquaticus

Seq: 430 a.a.

Struc: 297 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.5.4 - signal-recognition-particle GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

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

reference

DOI no: 10.1107/S0907444906040807

Acta Crystallogr D Biol Crystallogr 62:1520-1534 (2006)

PubMed id: 17139088

Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.

U.D.Ramirez, D.M.Freymann.

ABSTRACT

Two new structures of the SRP GTPase Ffh have been determined at 1.1 A resolution and provide the basis for comparative examination of the extensive water structure of the apo conformation of these GTPases. A set of well defined water-binding positions have been identified in the active site of the two-domain ;NG' GTPase, as well as at two functionally important interfaces. The water hydrogen-bonding network accommodates alternate conformations of the protein side chains by undergoing local rearrangements and, in one case, illustrates binding of a solute molecule within the active site by displacement of water molecules without further disruption of the water-interaction network. A subset of the water positions are well defined in several lower resolution structures, including those of different nucleotide-binding states; these appear to function in maintaining the protein structure. Consistent arrangements of surface water between three different ultrahigh-resolution structures provide a framework for beginning to understand how local water structure contributes to protein-ligand and protein-protein binding in the SRP GTPases.

Selected figure(s)

Figure 1.
Figure 1 Features of the electron-density maps that reflect alternate conformations. (a) Before (left) and after (right) modeling alternate configurations of residues 126-129 in structure IIA. The 2F[o] - F[c] map contoured at 1 is shown in light blue, the negative difference map (F[o] - F[c] contoured at -3 ) shown in red and the positive difference map (contoured at 3 ) shown in bright blue. The same maps are shown at the same contour levels after the addition of alternates and are superimposed on the model of residues 126-129 with alternate conformations (shaded blue). The alternate side-chain positions are indicated by asterisks. The `backrub' motion of Arg127 (Davis et al., 2006[Davis, I. W., Arendall, W. B. III, Richardson, D. C. & Richardson, J. S. (2006). Structure, 14, 265-274.]) is indicated by two arrows. A significant translation of the peptide perpendicular to the viewer is obscured in this orientation (see Fig. 2-a). (b) A peptide flip between Gln107 and Gly108 of the motif I P-loop in structure IIA. Note the water hydrogen bonded to the `flipped' configuration of the Gly108 amide nitrogen. There is an `unexplained' density (likely to be a buffer molecule) bound within the P-loop (at the center). (c) Two conformations of the conserved DARGG loop, the first in structure IA and the second in structure IIA.

Figure 4.
Figure 4 Details of the water structure. (a) The water structure at the solvent-exposed edge of a pocket of hydrophobic residues is shown. Water molecules shown in red (470, 527, 569, 614 and 1709) participate in a water pentamer. The pentamer fills the groove along the surface of the protein that is formed by the side chains of residues extending into the hydrophobic pocket below the surface. Hydrogen bonds made among the members of the pentamer are shown as red dotted lines and hydrogen bonds from pentamer members to protein residues are shown as black dotted lines. The surrounding water structure and the hydrogen bonds these waters make are shown in blue. Alternate conformations of protein and water molecules in this region are omitted for clarity. (b) Stereo image of the acetate molecule bound within the active site in structure I, the waters in structure II that occupy the space of the acetate (superimposed, yellow) and the residues which hydrogen bond to them. Hydrogen bonds from the acetate O atoms are shown as red dotted lines and the waters of structure II are shown in yellow, as are the dotted lines representing the hydrogen bonds they make with each other and with protein atoms.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1520-1534) copyright 2006.

Figures were selected by the author.