4LCL

Simvastatin Synthase (LOVD), from Aspergillus Terreus, LovD6 mutant (simh6208)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The role of distant mutations and allosteric regulation on LovD active site dynamics.

Jimenez-Oses, G.Osuna, S.Gao, X.Sawaya, M.R.Gilson, L.Collier, S.J.Huisman, G.W.Yeates, T.O.Tang, Y.Houk, K.N.

(2014) Nat Chem Biol 10: 431-436

  • DOI: 10.1038/nchembio.1503
  • Primary Citation of Related Structures:  
    4LCL, 4LCM

  • PubMed Abstract: 
  • Natural enzymes have evolved to perform their cellular functions under complex selective pressures, which often require their catalytic activities to be regulated by other proteins. We contrasted a natural enzyme, LovD, which acts on a protein-bound (LovF) acyl substrate, with a laboratory-generated variant that was transformed by directed evolution to accept instead a small free acyl thioester and no longer requires the acyl carrier protein ...

    Natural enzymes have evolved to perform their cellular functions under complex selective pressures, which often require their catalytic activities to be regulated by other proteins. We contrasted a natural enzyme, LovD, which acts on a protein-bound (LovF) acyl substrate, with a laboratory-generated variant that was transformed by directed evolution to accept instead a small free acyl thioester and no longer requires the acyl carrier protein. The resulting 29-mutant variant is 1,000-fold more efficient in the synthesis of the drug simvastatin than the wild-type LovD. This is to our knowledge the first nonpatent report of the enzyme currently used for the manufacture of simvastatin as well as the intermediate evolved variants. Crystal structures and microsecond-scale molecular dynamics simulations revealed the mechanism by which the laboratory-generated mutations free LovD from dependence on protein-protein interactions. Mutations markedly altered conformational dynamics of the catalytic residues, obviating the need for allosteric modulation by the acyl carrier LovF.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransesteraseA, B433Aspergillus terreusMutation(s): 22 
Gene Names: lovD
EC: 2.3.1.238
UniProt
Find proteins for Q9Y7D1 (Aspergillus terreus)
Explore Q9Y7D1 
Go to UniProtKB:  Q9Y7D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y7D1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.8α = 90
b = 76.39β = 93.91
c = 113.76γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-05-28
    Changes: Database references
  • Version 1.3: 2014-06-04
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description