8GYI image
Deposition Date 2022-09-22
Release Date 2023-02-22
Last Version Date 2023-11-29
Entry Detail
PDB ID:
8GYI
Title:
Crystal structure of Fic25 (holo form) from Streptomyces ficellus
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.93 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 65
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DegT/DnrJ/EryC1/StrS family aminotransferase
Gene (Uniprot):EIZ62_06105
Chain IDs:A, B
Chain Length:439
Number of Molecules:2
Biological Source:Streptomyces ficellus
Primary Citation
Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
Acs Chem.Biol. 18 385 395 (2023)
PMID: 36669120 DOI: 10.1021/acschembio.2c00823

Abstact

(2,6)-Diamino-(5,7)-dihydroxyheptanoic acid (DADH), a non-proteinogenic amino acid, is converted to 1-azabicyclo[3.1.0]hexane ring-containing amino acids that are subsequently incorporated into ficellomycin and vazabitide A. The present study revealed that the sugar aminotransferase-like enzymes Fic25 and Vzb9, with a high amino acid sequence identity (56%) to each other, synthesized stereoisomers of DADH with (6S) and (6R) configurations, respectively. The crystal structure of the Fic25 complex with a PLP-(6S)-N2-acetyl-DADH adduct indicated that Asn45 and Gln197 (Asn205 and Ala53 in Vzb9) were located at positions that affected the stereochemistry of DADH being synthesized. A modeling study suggested that amino acid substitutions between Fic25 and Vzb9 allowed the enzymes to bind to the substrate with almost 180° rotation in the C5-C7 portions of the DADH molecules, accompanied by a concomitant shift in their C1-C4 portions. In support of this result, the replacement of two corresponding residues in Fic25 and Vzb9 increased (6R) and (6S) stereoselectivities, respectively. The different stereochemistry at C6 of DADH resulted in a different stereochemistry/orientation of the aziridine portion of the 1-azabicyclo[3.1.0]hexane ring, which plays a crucial role in biological activity, between ficellomycin and vazabitide A. A phylogenic analysis suggested that Fic25 and Vzb9 evolved from sugar aminotransferases to produce unusual building blocks for expanding the structural diversity of secondary metabolites.

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