4A2S
Structure of the engineered retro-aldolase RA95.5
Summary for 4A2S
| Entry DOI | 10.2210/pdb4a2s/pdb |
| Related | 1A53 1IGS 1JUK 1JUL 1LBF 1LBL 2C3Z 4A2R |
| Descriptor | INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE, 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE (3 entities in total) |
| Functional Keywords | lyase, engineered enzyme, directed evolution |
| Biological source | SULFOLOBUS SOLFATARICUS |
| Total number of polymer chains | 1 |
| Total formula weight | 30233.84 |
| Authors | |
| Primary citation | Giger, L.,Caner, S.,Obexer, R.,Kast, P.,Baker, D.,Ban, N.,Hilvert, D. Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat.Chem.Biol., 9:494-498, 2013 Cited by PubMed Abstract: Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that pronounced molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400-fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate-binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. PubMed: 23748672DOI: 10.1038/nchembio.1276 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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