PDBsum entry 1yyr

Lyase

PDB id: 1yyr

Contents

Protein chains

353 a.a. *

Ligands

SAZ ×2

EDO ×2

POP

Metals

_MG ×3

Waters ×46

* Residue conservation analysis

PDB id:

1yyr

Name:

Lyase

Title:

Y305f trichodiene synthase: complex with mg, pyrophosphate, and (4r)- 7-azabisabolene

Structure:

Trichodiene synthase. Chain: a, b. Synonym: sesquiterpene cyclase, ts. Engineered: yes. Mutation: yes

Source:

Fusarium sporotrichioides. Organism_taxid: 5514. Gene: tri5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.219 R-free: 0.255

Authors:

L.S.Vedula,M.J.Rynkiewicz,H.J.Pyun,R.M.Coates,D.E.Cane, D.W.Christianson

Key ref:

L.S.Vedula et al. (2005). Molecular recognition of the substrate diphosphate group governs product diversity in trichodiene synthase mutants. Biochemistry, 44, 6153-6163. PubMed id: 15835903 DOI: 10.1021/bi050059o

Date:

25-Feb-05 Release date: 29-Mar-05

Protein chains

P13513  (TRI5_FUSSP) -  Trichodiene synthase from Fusarium sporotrichioides

Seq: 374 a.a.

Struc: 353 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.3.6 - trichodiene synthase.
• Pathway: Bisabolene derived sesquiterpenoid biosynthesis
• Reaction: (2E,6E)-farnesyl diphosphate = trichodiene + diphosphate

(2E,6E)-farnesyl diphosphate = trichodiene (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi050059o

Biochemistry 44:6153-6163 (2005)

PubMed id: 15835903

Molecular recognition of the substrate diphosphate group governs product diversity in trichodiene synthase mutants.

L.S.Vedula, M.J.Rynkiewicz, H.J.Pyun, R.M.Coates, D.E.Cane, D.W.Christianson.

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.