4H69

Crystal Structure of the Allene Oxide Cyclase 2 from Physcomitrella patens complexed with substrate analog

Summary for 4H69

• Entry DOI: 10.2210/pdb4h69/pdb
• Related: 4H6A 4H6B 4H6C
• Descriptor: Allene oxide cyclase, PHOSPHATE ION, (9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid, ... (5 entities in total)
• Functional Keywords: b-barrel, oxylipins, fatty acid, metabolites, allene-oxide cyclase activity, isomerase
• Biological source: Physcomitrella patens
• Total number of polymer chains: 6
• Total formula weight: 127690.33

Authors

Neumann, P.,Ficner, R. (deposition date: 2012-09-19, release date: 2012-10-17, Last modification date: 2024-04-03)

Primary citation

Neumann, P.,Brodhun, F.,Sauer, K.,Herrfurth, C.,Hamberg, M.,Brinkmann, J.,Scholz, J.,Dickmanns, A.,Feussner, I.,Ficner, R.
Crystal Structures of Physcomitrella patens AOC1 and AOC2: Insights into the Enzyme Mechanism and Differences in Substrate Specificity.
Plant Physiol., 160:1251-1266, 2012

PubMed Abstract: In plants, oxylipins regulate developmental processes and defense responses. The first specific step in the biosynthesis of the cyclopentanone class of oxylipins is catalyzed by allene oxide cyclase (AOC) that forms cis(+)-12-oxo-phytodienoic acid. The moss Physcomitrella patens has two AOCs (PpAOC1 and PpAOC2) with different substrate specificities for C₁₈- and C₂₀-derived substrates, respectively. To better understand AOC's catalytic mechanism and to elucidate the structural properties that explain the differences in substrate specificity, we solved and analyzed the crystal structures of 36 monomers of both apo and ligand complexes of PpAOC1 and PpAOC2. From these data, we propose the following intermediates in AOC catalysis: (1) a resting state of the apo enzyme with a closed conformation, (2) a first shallow binding mode, followed by (3) a tight binding of the substrate accompanied by conformational changes in the binding pocket, and (4) initiation of the catalytic cycle by opening of the epoxide ring. As expected, the substrate dihydro analog cis-12,13S-epoxy-9Z,15Z-octadecadienoic acid did not cyclize in the presence of PpAOC1; however, when bound to the enzyme, it underwent isomerization into the corresponding trans-epoxide. By comparing complex structures of the C₁₈ substrate analog with in silico modeling of the C₂₀ substrate analog bound to the enzyme allowed us to identify three major molecular determinants responsible for the different substrate specificities (i.e. larger active site diameter, an elongated cavity of PpAOC2, and two nonidentical residues at the entrance of the active site).

PubMed: 22987885
DOI: 10.1104/pp.112.205138

Experimental method

X-RAY DIFFRACTION (2 Å)