2FCM

X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group

Summary for 2FCM

• Entry DOI: 10.2210/pdb2fcm/pdb
• Related: 1YIW 1YJ1 2fcn 2fcq 2fcs
• Descriptor: Ubiquitin, CADMIUM ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: ubiquitin, structural protein
• Total number of polymer chains: 2
• Total formula weight: 18389.53

Authors

Bang, D.,Gribenko, A.V.,Tereshko, V.,Kossiakoff, A.A.,Kent, S.B.,Makhatadze, G.I. (deposition date: 2005-12-12, release date: 2006-01-31, Last modification date: 2024-10-30)

Primary citation

Bang, D.,Gribenko, A.V.,Tereshko, V.,Kossiakoff, A.A.,Kent, S.B.,Makhatadze, G.I.
Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.
Nat.Chem.Biol., 2:139-143, 2006

PubMed 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.

PubMed: 16446709
DOI: 10.1038/nchembio766

Experimental method

X-RAY DIFFRACTION (2.2 Å)