4QPZ

Crystal structure of the formolase FLS_v2 in space group P 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational protein design enables a novel one-carbon assimilation pathway.

Siegel, J.B.Smith, A.L.Poust, S.Wargacki, A.J.Bar-Even, A.Louw, C.Shen, B.W.Eiben, C.B.Tran, H.M.Noor, E.Gallaher, J.L.Bale, J.Yoshikuni, Y.Gelb, M.H.Keasling, J.D.Stoddard, B.L.Lidstrom, M.E.Baker, D.

(2015) Proc.Natl.Acad.Sci.USA 112: 3704-3709

  • DOI: 10.1073/pnas.1500545112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixa ...

    We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.


    Organizational Affiliation

    Department of Chemistry, Department of Biochemistry and Molecular Medicine, and Genome Center, University of California, Davis, CA 95616; Department of Biochemistry and the Institute for Protein Design, Biomolecular Structure and Design Program.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formolase
A, B, C, D, E, F, G, H
582Pseudomonas fluorescensMutation(s): 0 
Gene Names: bznB
Find proteins for Q9F4L3 (Pseudomonas fluorescens)
Go to UniProtKB:  Q9F4L3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.878α = 90.00
b = 136.564β = 95.36
c = 167.062γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references