Yellow fluorescent protein phiYFPv (Phialidium): Structure and structure-based mutagenesis

Nadya V. Pletneva, Vladimir Z. Pletnev, Ekaterina Souslova, Dmitry M. Chudakov, Sergey Lukyanov, Vladimir I. Martynov, Svetlena Arhipova, Igor Artemyev, Alexander Wlodawer, Zbigniew Dauter, Sergei Pletnev

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16 Citations (Scopus)


The yellow fluorescent protein phiYFPv (λem max ≃ 537 14;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 14;nm). Here, the crystal structure of phiYFPv has been determined at 2.05 14;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 14;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.

Original languageEnglish
Pages (from-to)1005-1012
Number of pages8
JournalActa Crystallographica Section D: Biological Crystallography
Issue number6
Publication statusPublished - Jun 2013
Externally publishedYes


  • chromophores
  • intersubunit surface
  • oligomeric structure
  • Phialidium
  • structure-function relationship
  • yellow fluorescent protein


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