4DXP
Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X121
Summary for 4DXP
| Entry DOI | 10.2210/pdb4dxp/pdb |
| Related | 4DXI 4DXM 4DXN 4DXO 4DXQ |
| Descriptor | LEA X121 GFP-LIKE PROTEINS, MAGNESIUM ION (3 entities in total) |
| Functional Keywords | beta barrel, luminescent protein |
| Biological source | Synthetic Construct (artificial) |
| Total number of polymer chains | 1 |
| Total formula weight | 26531.75 |
| Authors | Kim, H.,Fromme, R.,Wachter, R.M. (deposition date: 2012-02-27, release date: 2013-02-27, Last modification date: 2023-11-15) |
| Primary citation | Kim, H.,Zou, T.,Modi, C.,Dorner, K.,Grunkemeyer, T.J.,Chen, L.,Fromme, R.,Matz, M.V.,Ozkan, S.B.,Wachter, R.M. A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure, 23:34-43, 2015 Cited by PubMed Abstract: In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities. PubMed: 25565105DOI: 10.1016/j.str.2014.11.011 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.75 Å) |
Structure validation
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