7XKX

Crystal structure of Tpn2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure-guided product determination of the bacterial type II diterpene synthase Tpn2.

Stowell, E.A.Ehrenberger, M.A.Lin, Y.L.Chang, C.Y.Rudolf, J.D.

(2022) Commun Chem 5: 146-146

  • DOI: https://doi.org/10.1038/s42004-022-00765-6
  • Primary Citation of Related Structures:  
    7XKX

  • PubMed Abstract: 

    A grand challenge in terpene synthase (TS) enzymology is the ability to predict function from protein sequence. Given the limited number of characterized bacterial TSs and significant sequence diversities between them and their eukaryotic counterparts, this is currently impossible. To contribute towards understanding the sequence-structure-function relationships of type II bacterial TSs, we determined the structure of the terpentedienyl diphosphate synthase Tpn2 from Kitasatospora sp. CB02891 by X-ray crystallography and made structure-guided mutants to probe its mechanism. Substitution of a glycine into a basic residue changed the product preference from the clerodane skeleton to a syn-labdane skeleton, resulting in the first syn-labdane identified from a bacterial TS. Understanding how a single residue can dictate the cyclization pattern in Tpn2, along with detailed bioinformatics analysis of bacterial type II TSs, sets the stage for the investigation of the functional scope of bacterial type II TSs and the discovery of novel bacterial terpenoids.


  • Organizational Affiliation

    Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SQHop_cyclase_C domain-containing protein
A, B
532Kitasatospora sp. CB02891Mutation(s): 0 
Gene Names: CG736_03410
UniProt
Find proteins for A0A2M9LDX2 (Kitasatospora sp. CB02891)
Explore A0A2M9LDX2 
Go to UniProtKB:  A0A2M9LDX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2M9LDX2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.539α = 90
b = 92.539β = 90
c = 127.911γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-A49-026-MY3
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00 GM124461
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM142574

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description