Three-Dimensional Structure of Yellow Fluorescent Protein Zyfp538 from Zoanthus Sp. at the Resolution 1.8 Å

N. V. Pletneva1 #, S. V. Pletnev3, D. M. Chudakov1, T. V. Tikhonova2, V. O. Popov2, V. I. Martynov2, A. Wlodawer4, Z. Dauter3 and V. Z. Pletnev1

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1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia;
2Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii pr. 33, Moscow, 119071, Russia;
3Synchrotron Radiation Research Section, Laboratory of Macromolecular Crystallography, National Cancer Institute, Argonne, IL 60439, USA;
4Protein Structure Section, Laboratory of Macromolecular Crystallography, National Cancer Institute, Frederick, MD 21702, USA

Received: January 18, 2007;  in final form: January 22, 2007

Abstract.  The three-dimensional structure of yellow fluorescent proteins zYFP538 (zFP538) from the button polyp Zoanthus sp. was determined at a resolution of 1.8 Å by X-ray analysis. The monomer of zYFP538 adopts a structure characteristic of the green fluorescent protein (GFP) family, a β-barrel formed from 11 antiparallel β segments and one internal α helix with a chromophore embedded into it. Like the TurboGFP, the β-barrel of zYFP538 contains a water-filled pore leading to the chromophore Tyr67 residue, which presumably provides access of molecular oxygen necessary for the maturation process. The post-translational modification of the chromophore-forming triad Lys66-Tyr67-Gly68 results in a tricyclic structure consisting of a five-membered imidazolinone ring, a phenol ring of the Tyr67 residue, and an additional six-membered tetrahydropyridine ring. The chromophore formation is completed by cleavage of the protein backbone at the C α-N bond of Lys66. It was suggested that the energy conflict between the buried positive charge of the intact Lys66 side chain in the hydrophobic pocket formed by the Ile44, Leu46, Phe65, Leu204 and Leu219 side chains is the most probable trigger that induces the transformation of the bicyclic green form to the tricyclic yellow form. A stereochemical analysis of the contacting surfaces at the intratetramer interfaces helped reveal a group of conserved key residues responsible for the oligomerization. Along with others, these residues should be taken into account in designing monomeric forms suitable for practical application as markers of proteins and cell organelles.

Key words:  GFP-like proteins, crystal structure, chromophore structure, tetramer structure, intersubunit interfaces, yellow fluorescent protein, Zoanthus sp.

Russian Journal of Bioorganic Chemistry 2007, 33 (4): 390-398