PDBsum entry 1v80

Signaling protein

PDB id: 1v80

Contents

Protein chain

76 a.a. *

* Residue conservation analysis

PDB id:

1v80

Name:

Signaling protein

Title:

Solution structures of ubiquitin at 30 bar and 3 kbar

Structure:

Ubiquitin/60s ribosomal protein l40 fusion. Chain: a

Source:

Bos taurus. Cattle. Organism_taxid: 9913

NMR struc:

10 models

Authors:

R.Kitahara,S.Yokoyama,K.Akasaka,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

R.Kitahara et al. (2005). NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar. J Mol Biol, 347, 277-285. PubMed id: 15740740 DOI: 10.1016/j.jmb.2005.01.052

Date:

27-Dec-03 Release date: 15-Feb-05

Protein chain

P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus

Seq: 690 a.a.

Struc: 76 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2005.01.052

J Mol Biol 347:277-285 (2005)

PubMed id: 15740740

NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.

R.Kitahara, S.Yokoyama, K.Akasaka.

ABSTRACT

Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation. The method utilizes the intimate relationship between conformation and partial molar volume and determines three-dimensional structures of a protein at different pressures using variable pressure NMR technique, whereby NOE distance and torsion angle constraints are used to create average coordinates. Ubiquitin (pH 4.6 at 20 degrees C) was chosen as the first target, for which structures were determined at 30 bar and at 3 kbar, giving "NMR snapshots" of a fluctuating protein structure at atomic resolution. The result reveals that the helix swings in and out by >3 angstroms with a simultaneous reorientation of the C-terminal segment, providing an "open" conformer suitable for enzyme recognition. Spin relaxation analysis indicates that this fluctuation occurs in the ten microsecond time range with activation volumes -4.2(+/-3.2) and 18.5(+/-3.0) ml/mol for the "closed-to-open" and the "open-to-closed" transitions, respectively.

Selected figure(s)

Figure 3.
Figure 3. Molecular surface of ubiquitin at 30 bar (a) and at 3 kbar (b). Calculation was performed on selected energy-minimized structures of ubiquitin (pH 4.6, 20 8C) using the program GRASP 24 with a probe radius of 1.4 Å .

Figure 4.
Figure 4. Spin relaxation dynamics of ubiquitin at 30 bar (open circle) and at 3 kbar (filled circle). (a) 15 N longitudinal relaxation rates, 15 N-R1. (b) 15 N transverse relaxation rates, 15 N- R2. (c) 1 H-induced 15 N nuclear Overhauser effect, 15 N{ 1 H}-NOE. (a)--(c) Data are not included for E24 and G53 (due to severe line- broadening), for D21 and A28 (due to spectral overlap at 30 bar), for E16 and V26 (due to spectral overlap at 3 kbar), for I36 (due to signal disappearance at 3 kbar), and for the Pro residues (P19, P37, P38) with no amide groups. (d) Order parameters of N--H vectors, S 2 . (e) Exchange contribution to 15 N transverse relaxation rates, 15 N-Rex. Plots in (d) and (e) were obtained from the Modelfree analysis 25,26 of the spin relaxation parameters for ubiquitin (pH 4.6 at 20 8C) with the program FAST-Modelfree 26 under the assumption of isotropic molecular tumbling. The overall rotational correlation times were 4.7 ns both at 30 bar and at 3 kbar. Relaxation parameters for resi- dues 4, 23, 25, 32, 35 and 49 at 30 bar and residues 2, 4, 9, 13, 14, 17, 28, 29, 32, 43 and 54 at 3 kbar do not show a reasonable fit to the Modelfree analysis, giving no data in (d) and (e).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 347, 277-285) copyright 2005.

Figures were selected by an automated process.