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TitleMicroED Structure of a Protoglobin Reactive Carbene Intermediate.
Journal, issue, pagesJ Am Chem Soc, Vol. 145, Issue 13, Page 7159-7165, Year 2023
Publish dateApr 5, 2023
AuthorsEmma Danelius / Nicholas J Porter / Johan Unge / Frances H Arnold / Tamir Gonen /
PubMed AbstractMicrocrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of ...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.
External linksJ Am Chem Soc / PubMed:36948184 / PubMed Central
MethodsEM (electron crystallography)
Resolution2.1 - 2.5 Å
Structure data

28615

8eum

EMDB-28615, PDB-8eum:
MicroED structure of an Aeropyrum pernix protoglobin mutant
Method: EM (electron crystallography) / Resolution: 2.1 Å

28616

8eun

EMDB-28616, PDB-8eun:
MicroED structure of an Aeropyrum pernix protoglobin metallo-carbene complex
Method: EM (electron crystallography)

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-IMD:
IMIDAZOLE

ChemComp-FE:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-WUF:
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

Source
  • aeropyrum pernix (archaea)
KeywordsMETAL BINDING PROTEIN / MicroED / protoglobin / directed evolution

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