3G4D

Crystal Structure of (+)-delta-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis

Summary for 3G4D

• Entry DOI: 10.2210/pdb3g4d/pdb
• Related: 3G4F
• Descriptor: (+)-delta-cadinene synthase isozyme XC1, BETA-MERCAPTOETHANOL, GLYCEROL, ... (4 entities in total)
• Functional Keywords: cyclase, lyase, magnesium, metal-binding
• Biological source: Gossypium arboreum (tree cotton)
• Total number of polymer chains: 2
• Total formula weight: 129038.07

Authors

Gennadios, H.A.,Di Costanzo, L.,Miller, D.J.,Allemann, R.K.,Christianson, D.W. (deposition date: 2009-02-03, release date: 2009-06-16, Last modification date: 2023-09-06)

Primary citation

Gennadios, H.A.,Gonzalez, V.,Di Costanzo, L.,Li, A.,Yu, F.,Miller, D.J.,Allemann, R.K.,Christianson, D.W.
Crystal structure of (+)-delta-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis.
Biochemistry, 48:6175-6183, 2009

PubMed Abstract: (+)-Delta-cadinene synthase (DCS) from Gossypium arboreum (tree cotton) is a sesquiterpene cyclase that catalyzes the cyclization of farnesyl diphosphate in the first committed step of the biosynthesis of gossypol, a phytoalexin that defends the plant from bacterial and fungal pathogens. Here, we report the X-ray crystal structure of unliganded DCS at 2.4 A resolution and the structure of its complex with three putative Mg(2+) ions and the substrate analogue inhibitor 2-fluorofarnesyl diphosphate (2F-FPP) at 2.75 A resolution. These structures illuminate unusual features that accommodate the trinuclear metal cluster required for substrate binding and catalysis. Like other terpenoid cyclases, DCS contains a characteristic aspartate-rich D(307)DTYD(311) motif on helix D that interacts with Mg(2+)(A) and Mg(2+)(C). However, DCS appears to be unique among terpenoid cyclases in that it does not contain the "NSE/DTE" motif on helix H that specifically chelates Mg(2+)(B), which is usually found as the signature sequence (N,D)D(L,I,V)X(S,T)XXXE (boldface indicates Mg(2+)(B) ligands). Instead, DCS contains a second aspartate-rich motif, D(451)DVAE(455), that interacts with Mg(2+)(B). In this regard, DCS is more similar to the isoprenoid chain elongation enzyme farnesyl diphosphate synthase, which also contains two aspartate-rich motifs, rather than the greater family of terpenoid cyclases. Nevertheless, the structure of the DCS-2F-FPP complex shows that the structure of the trinuclear magnesium cluster is generally similar to that of other terpenoid cyclases despite the alternative Mg(2+)(B) binding motif. Analyses of DCS mutants with alanine substitutions in the D(307)DTYD(311) and D(451)DVAE(455) segments reveal the contributions of these segments to catalysis.

PubMed: 19489610
DOI: 10.1021/bi900483b

Experimental method

X-RAY DIFFRACTION (2.403 Å)