4OPU

Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.

Kung, Y.McAndrew, R.P.Xie, X.Liu, C.C.Pereira, J.H.Adams, P.D.Keasling, J.D.

(2014) Structure 22: 1028-1036

  • DOI: 10.1016/j.str.2014.05.007
  • Primary Citation of Related Structures:  
    4OPT, 4OPG, 4OPI, 4OPL, 4OPC, 4OPD, 4OPU

  • PubMed Abstract: 
  • The archaeal enzyme geranylgeranyl reductase (GGR) catalyzes hydrogenation of carbon-carbon double bonds to produce the saturated alkyl chains of the organism's unusual isoprenoid-derived cell membrane. Enzymatic reduction of isoprenoid double bonds ...

    The archaeal enzyme geranylgeranyl reductase (GGR) catalyzes hydrogenation of carbon-carbon double bonds to produce the saturated alkyl chains of the organism's unusual isoprenoid-derived cell membrane. Enzymatic reduction of isoprenoid double bonds is of considerable interest both to natural products researchers and to synthetic biologists interested in the microbial production of isoprenoid drug or biofuel molecules. Here we present crystal structures of GGR from Sulfolobus acidocaldarius, including the structure of GGR bound to geranylgeranyl pyrophosphate (GGPP). The structures are presented alongside activity data that depict the sequential reduction of GGPP to H6GGPP via the intermediates H2GGPP and H4GGPP. We then modified the enzyme to generate sequence variants that display increased rates of H6GGPP production or are able to halt the extent of reduction at H2GGPP and H4GGPP. Crystal structures of these variants not only reveal the structural bases for their altered activities; they also shed light onto the catalytic mechanism employed.


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: jdkeasling@lbl.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved Archaeal proteinA453Sulfolobus acidocaldarius DSM 639Mutation(s): 1 
Gene Names: Saci_0986
EC: 1.3.1.83 (PDB Primary Data), 1.3 (UniProt)
Find proteins for Q4JA33 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JA33 
Go to UniProtKB:  Q4JA33
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download Ideal Coordinates CCD File 
A
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
GRG
Query on GRG

Download Ideal Coordinates CCD File 
A
GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.921α = 90
b = 81.988β = 90
c = 106.169γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references