PDBsum entry 2fcs

Structural protein

PDB id: 2fcs

Contents

Protein chains

73 a.a. *

Ligands

ACT ×3

_CD ×7

SO4

Waters ×123

* Residue conservation analysis

PDB id:

2fcs

Name:

Structural protein

Title:

X-ray crystal structure of a chemically synthesized [l-gln35]ubiquitin with a cubic space group

Structure:

Ubiquitin. Chain: a, b. Fragment: residues 1-76. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of the protein can be naturally found in homo sapiens (human)

Resolution:

1.80Å R-factor: 0.207 R-free: 0.236

Authors:

D.Bang,A.V.Gribenko,V.Tereshko,A.A.Kossiakoff,S.B.Kent,G.I.Makhatadze

Key ref:

D.Bang et al. (2006). Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat Chem Biol, 2, 139-143. PubMed id: 16446709 DOI: 10.1038/nchembio766

Date:

12-Dec-05 Release date: 31-Jan-06

Protein chains

No UniProt id for this chain

Struc: 73 a.a.

DOI no: 10.1038/nchembio766

Nat Chem Biol 2:139-143 (2006)

PubMed id: 16446709

Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.

D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, G.I.Makhatadze.

ABSTRACT

The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of this residue in a left-handed conformation or enhanced solvation of the peptide backbone because of the absence of a side chain. Attempts to quantify the contributions of these two effects have been made previously, but the issue remains unresolved. Here we have used chemical protein synthesis to dissect the energetic basis of alpha-helix termination by comparing a series of ubiquitin variants containing an L-amino acid or the corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can adopt a left-handed conformation without energetic penalty, so the contributions of conformational strain and backbone solvation can thus be separated. Analysis of the thermodynamic data revealed that the preference for glycine at the C' position of a helix is predominantly a conformational effect.

Selected figure(s)

Figure 1.
The -helix encompassing residues 24–33 is highlighted in cyan; the C' Gly35 residue in the C-cap region in the wild-type protein is shown in space-filling CPK representation.

Figure 2.
Top and middle, the C atom traces of the four proteins (15 crystallographically independent structures) are superimposed: wild-type ubiquitin (three molecules from orthorhombic P2[1]2[1]2[1] space group^*, gray); [D-Gln35]ubiquitin (three molecules from P2[1]2[1]2[1]^*, red, and two molecules from cubic P4[3]32 space group, pink); [D-Val35]ubiquitin (two molecules from P4[3]32, green); and [L-Gln35]ubiquitin (two molecules from P4[3]32, yellow). All C atoms were used in the superposition. Residue 35 is marked with a black arrow. Side views are shown in the top panels and top views in the middle panels. Bottom, superposition of ten residues (residue 30–39) near residue 35. The main-chain atoms of the four X-ray structures are shown: wild-type ubiquitin (P2[1]2[1]2[1]^*, gray); [D-Gln35]ubiquitin (P4[3]32, pink); [D-Val35]ubiquitin (P4[3]32, green); and [L-Gln35]ubiquitin (P4[3]32, yellow). The main-chain conformation of residues 30–39 is very similar in all four structures (r.m.s. deviations <0.2 Å), and only one molecule from each crystal form is shown for clarity. ^* denotes ubiquitin molecules taken from our previously reported structures in P2[1]2[1]2[1] space group: orthorhombic wild-type ubiquitin (PDB accession code 1YIW) and orthorhombic [D-Gln35]ubiquitin (1YJ1), both of whose structures have been deposited previously^13. The PDB codes for the cubic P4[3]32 structures of the four synthetic ubiquitins are listed in the Methods.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2006, 2, 139-143) copyright 2006.

Figures were selected by an automated process.