8EUN
MicroED structure of an Aeropyrum pernix protoglobin metallo-carbene complex
Summary for 8EUN
| Entry DOI | 10.2210/pdb8eun/pdb |
| Related | 8EUM |
| EMDB information | 28615 28616 |
| Descriptor | Protogloblin ApPgb, benzyl[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)di(propanoato)(2-)]iron (3 entities in total) |
| Functional Keywords | microed, directed evolution, metal binding protein |
| Biological source | Aeropyrum pernix |
| Total number of polymer chains | 2 |
| Total formula weight | 46853.01 |
| Authors | Danelius, E.,Gonen, T.,Unge, J.T. (deposition date: 2022-10-19, release date: 2023-04-05, Last modification date: 2024-05-22) |
| Primary citation | Danelius, E.,Porter, N.J.,Unge, J.,Arnold, F.H.,Gonen, T. MicroED Structure of a Protoglobin Reactive Carbene Intermediate. J.Am.Chem.Soc., 145:7159-7165, 2023 Cited by PubMed Abstract: Microcrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of small molecules, natural products, and peptides have been determined using methods. However, only a couple of novel protein structures have thus far been derived by MicroED. Taking advantage of recent technological advances, including higher acceleration voltage and using a low-noise detector in counting mode, we have determined the first structure of an protoglobin (Pgb) variant by MicroED using an AlphaFold2 model for phasing. The structure revealed that mutations introduced during directed evolution enhance carbene transfer activity by reorienting an α helix of Pgb into a dynamic loop, making the catalytic active site more readily accessible. After exposing the tiny crystals to the substrate, we also trapped the reactive iron-carbenoid intermediate involved in this engineered Pgb's new-to-nature activity, a challenging carbene transfer from a diazirine via a putative metallo-carbene. The bound structure discloses how an enlarged active site pocket stabilizes the carbene bound to the heme iron and, presumably, the transition state for the formation of this key intermediate. This work demonstrates that improved MicroED technology and the advancement in protein structure prediction now enable investigation of structures that was previously beyond reach. PubMed: 36948184DOI: 10.1021/jacs.2c12004 PDB entries with the same primary citation |
| Experimental method | ELECTRON CRYSTALLOGRAPHY (2.5 Å) |
Structure validation
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