8ZUT

Crystal structure of the F99S/M153T/V163A variant of GFP at pH 8.5

Summary for 8ZUT

• Entry DOI: 10.2210/pdb8zut/pdb
• Descriptor: Green fluorescent protein, MAGNESIUM ION (3 entities in total)
• Functional Keywords: green fluorescent protein, fluorescent protein
• Biological source: Aequorea victoria
• Total number of polymer chains: 1
• Total formula weight: 25892.57

Authors

Takeda, R.,Tsutsumi, E.,Takeda, K. (deposition date: 2024-06-10, release date: 2024-11-06)

Primary citation

Takeda, R.,Tsutsumi, E.,Okatsu, K.,Fukai, S.,Takeda, K.
Structural characterization of green fluorescent protein in the I-state.
Sci Rep, 14:22832-22832, 2024

PubMed Abstract: Green fluorescent protein (GFP) is widely utilized as a fluorescent tag in biochemical fields. Whereas the intermediate (I) state has been proposed in the photoreaction cycle in addition to the A and B states, until now the structure of I has only been estimated by computational studies. In this paper, we report the crystal structures of the I stabilizing variants of GFP at high resolutions where respective atoms can be observed separately. Comparison with the structures in the other states highlights the structural feature of the I state. The side chain of one of the substituted residues, Val203, adopts the gauche- conformation observed for Thr203 in the A state, which is different from the B state. On the other hand, His148 interacts with the chromophore by ordinary hydrogen bonding with a distance of 2.85 Å, while the weaker interaction by longer distances is observed in the A state. Therefore, it was indicated that it is possible to distinguish three states A, B and I by the two hydrogen bond distances Oγ-Thr203···Oη-chromophore and Nδ1-His148···Oη-chromophore. We discuss the characteristics of the I intermediate of wild-type GFP on the bases of the structure estimated from the variant structures by quantum chemical calculations.

PubMed: 39353998
DOI: 10.1038/s41598-024-73696-y

Experimental method

X-RAY DIFFRACTION (1.48 Å)