4QQ8 | pdb_00004qq8

Crystal structure of the formolase FLS in space group P 43 21 2

• PDB DOI: https://doi.org/10.2210/pdb4QQ8/pdb

• Classification: LYASE
• Organism(s): Pseudomonas fluorescens
• Mutation(s): No 


• Deposited: 2014-06-26 Released: 2015-03-11 
• Deposition Author(s): Shen, B.W., Siegel, J.B., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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 U S A 112: 3704-3709

• PubMed: 25775555 
• DOI: https://doi.org/10.1073/pnas.1500545112
• Primary Citation Related Structures: 
  4QPZ, 4QQ8


• 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 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.

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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.
Department of Chemical Engineering.
Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608;
Department of Biochemistry and the Institute for Protein Design.
Department of Plant Sciences, Weizmann Institute of Sciences, Rehovot 76100, Israel;
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;
Department of Biochemistry and the Institute for Protein Design, Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608;
Joint BioEnergy Institute, Emeryville, CA 94608; Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94550;
Department of Biochemistry and the Institute for Protein Design, Graduate Program in Molecular and Cellular Biology.
Department of Biochemistry and the Institute for Protein Design, Department of Energy, Joint Genome Institute, Lawrence National Berkeley Laboratory, Walnut Creek, CA 94598; Howard Hughes Medical Institute.
Department of Biochemistry and the Institute for Protein Design, Department of Chemistry, and.
Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608; QB3 Institute, University of California, Berkeley, CA 94270; Synthetic Biology Engineering Research Center, Emeryville, CA 94608; and Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94270.
Department of Chemical Engineering, Department of Microbiology, University of Washington, Seattle, WA 98195; [e-mail] [e-mail].
Department of Biochemistry and the Institute for Protein Design, Biomolecular Structure and Design Program, Howard Hughes Medical Institute, [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 247.82 kDa 
• Atom Count: 16,915 
• Modeled Residue Count: 2,264 
• Deposited Residue Count: 2,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formolase	A, B, C, D	583	Pseudomonas fluorescens	Mutation(s): 0  Gene Names: bznB
UniProt
Find proteins for Q9F4L3 (Pseudomonas fluorescens) Explore Q9F4L3  Go to UniProtKB:  Q9F4L3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	F [auth A], J [auth B], L [auth C], O [auth D]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
EDO	G [auth A], H [auth A], M [auth C], P [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.742	α = 90
b = 144.742	β = 90
c = 269.553	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Shen, B.W., Siegel, J.B., Stoddard, B.L.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description