5DW7

Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with alpha alpha Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.

Harris, G.G.Lombardi, P.M.Pemberton, T.A.Matsui, T.Weiss, T.M.Cole, K.E.Koksal, M.Murphy, F.V.Vedula, L.S.Chou, W.K.Cane, D.E.Christianson, D.W.

(2015) Biochemistry 54: 7142-7155

  • DOI: 10.1021/acs.biochem.5b01143
  • Primary Citation of Related Structures:  
    5DW7, 5DZ2

  • PubMed Abstract: 
  • Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction ...

    Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg(2+) for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg(2+) ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of ∼36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis.


    Organizational Affiliation

    Radcliffe Institute for Advanced Study, Harvard University , Cambridge, Massachusetts 02138, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Germacradienol/geosmin synthaseA366Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: cyc2SCO6073SC9B1.20
EC: 4.2.3.22 (PDB Primary Data), 4.2.3.75 (PDB Primary Data), 4.1.99.16 (PDB Primary Data)
UniProt
Find proteins for Q9X839 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9X839 
Go to UniProtKB:  Q9X839
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X839
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.78α = 90
b = 76.78β = 90
c = 130.599γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM56838
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM30301

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence