4HE4 image
Entry Detail
PDB ID:
4HE4
Title:
Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2012-10-03
Release Date:
2013-05-29
Method Details:
Experimental Method:
Resolution:
2.05 Å
R-Value Free:
0.25
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Yellow fluorescent protein
Chain IDs:A, B
Chain Length:246
Number of Molecules:2
Biological Source:Phialidium sp. SL-2003
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CRO A GLY ?
Primary Citation
Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis.
Acta Crystallogr.,Sect.D 69 1005 1012 (2013)
PMID: 23695245 DOI: 10.1107/S0907444913004034

Abstact

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.

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Primary Citation of related structures