8AFV

DaArgC3 - Engineered Formyl Phosphate Reductase with 3 substitutions (S178V, G182V, L233I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo.

Nattermann, M.Wenk, S.Pfister, P.He, H.Lee, S.H.Szymanski, W.Guntermann, N.Zhu, F.Nickel, L.Wallner, C.Zarzycki, J.Paczia, N.Gaissert, N.Francio, G.Leitner, W.Gonzalez, R.Erb, T.J.

(2023) Nat Commun 14: 2682-2682

  • DOI: https://doi.org/10.1038/s41467-023-38072-w
  • Primary Citation of Related Structures:  
    8AFU, 8AFV

  • PubMed Abstract: 

    Formate can be envisioned at the core of a carbon-neutral bioeconomy, where it is produced from CO 2 by (electro-)chemical means and converted into value-added products by enzymatic cascades or engineered microbes. A key step in expanding synthetic formate assimilation is its thermodynamically challenging reduction to formaldehyde. Here, we develop a two-enzyme route in which formate is activated to formyl phosphate and subsequently reduced to formaldehyde. Exploiting the promiscuity of acetate kinase and N-acetyl-γ-glutamyl phosphate reductase, we demonstrate this phosphate (P i )-based route in vitro and in vivo. We further engineer a formyl phosphate reductase variant with improved formyl phosphate conversion in vivo by suppressing cross-talk with native metabolism and interface the P i route with a recently developed formaldehyde assimilation pathway to enable C2 compound formation from formate as the sole carbon source in Escherichia coli. The P i route therefore offers a potent tool in expanding the landscape of synthetic formate assimilation.


  • Organizational Affiliation

    Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyl-gamma-glutamyl-phosphate reductase
A, B, C, D
342Denitrovibrio acetiphilus DSM 12809Mutation(s): 3 
Gene Names: argCDacet_0460
EC: 1.2.1.38
UniProt
Find proteins for D4H3H4 (Denitrovibrio acetiphilus (strain DSM 12809 / NBRC 114555 / N2460))
Explore D4H3H4 
Go to UniProtKB:  D4H3H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4H3H4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.877α = 90
b = 109.55β = 90
c = 133.225γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany031B0850B
German Research Foundation (DFG)Germany390919832

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Database references, Structure summary