4KAG

Crystal structure analysis of a single amino acid deletion mutation in EGFP

Summary for 4KAG

• Entry DOI: 10.2210/pdb4kag/pdb
• Related: 4KA9 4KEX
• Descriptor: Green fluorescent protein, 1,2-ETHANEDIOL, SULFATE ION, ... (5 entities in total)
• Functional Keywords: beta barrel, fluorescent protein, chromophore cyclisation, single amino acid deletion mutation
• Biological source: Aequorea victoria (Jellyfish)
• Total number of polymer chains: 1
• Total formula weight: 28393.00

Authors

Arpino, J.A.J.,Rizkallah, P.J. (deposition date: 2013-04-22, release date: 2014-08-06, Last modification date: 2024-10-16)

Primary citation

Arpino, J.A.,Rizkallah, P.J.,Jones, D.D.
Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein.
Acta Crystallogr.,Sect.D, 70:2152-2162, 2014

PubMed Abstract: Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP(D190Δ) containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP(A227Δ) revealed that a `flipping' mechanism was used to adjust for residue deletion at the end of a β-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.

PubMed: 25084334
DOI: 10.1107/S139900471401267X

Experimental method

X-RAY DIFFRACTION (1.12 Å)