4HE4

Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)

Summary for 4HE4

• Entry DOI: 10.2210/pdb4he4/pdb
• Related: 2OGR
• Descriptor: Yellow fluorescent protein (2 entities in total)
• Functional Keywords: phiyfp, yellow fluorescent protein, mutant variant of phiyfp, thr-tyr-gly chromophore, beta-barrel, biomarker, thr-tyr-gly bicyclic chromophore, fluorescent protein
• Biological source: Phialidium sp. SL-2003
• Total number of polymer chains: 2
• Total formula weight: 54216.77

Authors

Pletneva, N.,Pletnev, S.,Pletnev, V.Z. (deposition date: 2012-10-03, release date: 2013-05-29, Last modification date: 2024-11-06)

Primary citation

Pletneva, N.V.,Pletnev, V.Z.,Souslova, E.,Chudakov, D.M.,Lukyanov, S.,Martynov, V.I.,Arhipova, S.,Artemyev, I.,Wlodawer, A.,Dauter, Z.,Pletnev, S.
Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis.
Acta Crystallogr.,Sect.D, 69:1005-1012, 2013

PubMed Abstract: The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow-orange range (535-555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The `yellow' chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.

PubMed: 23695245
DOI: 10.1107/S0907444913004034

Experimental method

X-RAY DIFFRACTION (2.05 Å)