5ZM2 image
Deposition Date 2018-04-01
Release Date 2018-07-18
Last Version Date 2023-11-22
Entry Detail
PDB ID:
5ZM2
Keywords:
Title:
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.25
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Dioxygenase andA
Gene (Uniprot):andA
Chain IDs:A, B, C, D
Chain Length:306
Number of Molecules:4
Biological Source:Emericella variicolor
Primary Citation
Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis.
J. Am. Chem. Soc. 140 9743 9750 (2018)
PMID: 29972643 DOI: 10.1021/jacs.8b06084

Abstact

AndA, an Fe(II)/α-ketoglutarate (αKG)-dependent enzyme, is the key enzyme that constructs the unique and congested bridged-ring system of anditomin (1), by catalyzing consecutive dehydrogenation and isomerization reactions. Although we previously characterized AndA to some extent, the means by which the enzyme facilitates this drastic structural reconstruction have remained elusive. In this study, we have solved three X-ray crystal structures of AndA, in its apo form and in the complexes with Fe(II), αKG, and two substrates. The crystal structures and mutational experiments identified several key amino acid residues important for the catalysis and provided insight into how AndA controls the reaction. Furthermore, computational calculations validated the proposed reaction mechanism for the bridged-ring formation and also revealed the requirement of a series of conformational changes during the transformation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures