6K96 image
Deposition Date 2019-06-14
Release Date 2019-12-25
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6K96
Keywords:
Title:
Crystal structure of Ari2
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Five-membered-cyclitol-phosphate synthase
Gene (Uniprot):ari2
Chain IDs:A, B
Chain Length:378
Number of Molecules:2
Biological Source:Streptomyces citricolor
Primary Citation
Stereochemistry in the Reaction of themyo-Inositol Phosphate Synthase Ortholog Ari2 during Aristeromycin Biosynthesis.
Biochemistry 58 5112 5116 (2019)
PMID: 31825604 DOI: 10.1021/acs.biochem.9b00981

Abstact

The myo-inositol-1-phosphate synthase (MIPS) ortholog Ari2, which is encoded in the aristeromycin biosynthetic gene cluster, catalyzes the formation of five-membered cyclitol phosphate using d-fructose 6-phosphate (F6P) as a substrate. To understand the stereochemistry during the Ari2 reaction in vivo, we carried out feeding experiments with (6S)-d-[6-2H1]- and (6R)-d-[6-2H1]glucose in the aristeromycin-producing strain Streptomyces citricolor. We observed retention of the 2H atom of (6S)-d-[6-2H1]glucose and no incorporation of the 2H atom from (6R)-d-[6-2H1]glucose in aristeromycin. This indicates that Ari2 abstracts the pro-R proton at C6 of F6P after oxidation of C5-OH by nicotinamide adenine dinucleotide (NAD+) to generate the enolate intermediate, which then attacks the C2 ketone to form the C-C bond via aldol-type condensation. The reaction of Ari2 with (6S)-d-[6-2H1]- and (6R)-d-[6-2H1]F6P in vitro exhibited identical stereochemistry compared with that observed during the feeding experiments. Furthermore, analysis of the crystal structure of Ari2, including NAD+ as a ligand, revealed the active site of Ari2 to be similar to that of MIPS of Mycobacterium tuberculosis, supporting the similarity of the reaction mechanisms of Ari2 and MIPS.

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