1YYT

D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4R)-7-azabisabolene

Summary for 1YYT

• Entry DOI: 10.2210/pdb1yyt/pdb
• Related: 1JFA 1JFG 1KIY 1KIZ 1YJ4 1YYQ 1YYR 1YYS 1YYU
• Descriptor: Trichodiene synthase, (1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: terpenoid cyclase fold, site-directed mutant, pyrophosphate, (4r)-7-azabisabolene, lyase
• Biological source: Fusarium sporotrichioides
• Total number of polymer chains: 2
• Total formula weight: 88770.55

Authors

Vedula, L.S.,Rynkiewicz, M.J.,Pyun, H.J.,Coates, R.M.,Cane, D.E.,Christianson, D.W. (deposition date: 2005-02-25, release date: 2005-03-29, Last modification date: 2023-08-23)

Primary citation

Vedula, L.S.,Rynkiewicz, M.J.,Pyun, H.J.,Coates, R.M.,Cane, D.E.,Christianson, D.W.
Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants.
Biochemistry, 44:6153-6163, 2005

PubMed Abstract: The X-ray crystal structures of Y305F trichodiene synthase and its complex with coproduct inorganic pyrophosphate (PP(i)) and of Y305F and D100E trichodiene synthases in ternary complexes with PP(i) and aza analogues of the bisabolyl carbocation intermediate are reported. The Y305F substitution in the basic D(302)RRYR motif does not cause large changes in the overall structure in comparison with the wild-type enzyme in either the uncomplexed enzyme or its complex with PP(i). However, the loss of the Y305F-PP(i) hydrogen bond appears to be compensated by a very slight shift in the position of the side chain of R304. The putative bisabolyl carbocation mimic, R-azabisabolene, binds in a conformation and orientation that does not appear to mimic that of the actual carbocation intermediate, suggesting that the avid inhibition by R- and S-azabisabolenes arises more from favorable electrostatic interactions with PP(i) rather than any special resemblance to a reaction intermediate. Greater enclosed active-site volumes result from the Y305F and D100E mutations that appear to confer greater variability in ligand-binding conformations and orientations, which results in the formation of aberrant cyclization products. Because the binding conformations and orientations of R-azabisabolene to Y305F and D100E trichodiene synthases do not correspond to binding conformations required for product formation and because the binding conformations and orientations of diverse substrate and carbocation analogues to other cyclases such as 5-epi-aristolochene synthase and bornyl diphosphate synthase generally do not correspond to catalytically productive complexes, we conclude that the formation of transient carbocation intermediates in terpene cyclization reactions is generally under kinetic rather than thermodynamic control.

PubMed: 15835903
DOI: 10.1021/bi050059o

Experimental method

X-RAY DIFFRACTION (2.9 Å)