9V4C | pdb_00009v4c

Selective Production of Versatile L-Glyceraldehyde from C1 and/or C2 aldehydes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

From toxin to chiral building block: Engineered aldolase-catalyzed regioselective conversion of formaldehyde into L-glyceraldehyde.

Duysak, T.Kim, J.W.Seo, P.W.Woo, H.G.Park, J.B.Kim, J.S.

(2025) Int J Biol Macromol 331: 148343-148343

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.148343
  • Primary Citation of Related Structures:  
    9V4B, 9V4C

  • PubMed Abstract: 

    Formaldehyde (FALD) is a volatile and highly toxic compound widely used in industry and a major environmental pollutant due to its genotoxic and carcinogenic effects. Developing efficient methods to convert formaldehyde into value-added, non-toxic products is essential for both environmental protection and chemical sustainability. In this study, we present a biocatalytic cascade for the selective enzymatic conversion of formaldehyde into enantiopure L-glyceraldehyde, a high-value chiral C3 compound. The system employs a structurally engineered fructose-6-phosphate aldolase (GaFSA) from Gilliamella apicola, which catalyzes carbon-carbon bond formation via aldol condensation between glycolaldehyde (GALD) and formaldehyde. However, this system included a substantial portion of D-threose as a byproduct. By identifying Ser166 and Val203 as critical determinants of regioselectivity, structure-guided mutagenesis (S166R/V203S) suppressed D-threose formation and achieved >93 % selectivity under mild aqueous conditions. To avoid external GALD supplementation, the engineered GaFSA was coupled with an optimized glyoxylate carboligase from E. coli (EcGCL), enabling in situ GALD production from formaldehyde. This one-pot enzymatic cascade reached a conversion efficiency of ~94 % from 25 mM FALD at pH 7.5 and 40 °C, with minimal byproducts. The reaction proceeds entirely in water, under ambient pressure, without toxic reagents or organic solvents, requiring only natural cofactors for EcGCL activity. This work offers a sustainable enzymatic platform for formaldehyde detoxification and valorization, enabling selective C1-to-C3 upgrading and supporting greener chemical manufacturing.


  • Organizational Affiliation
    • Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Host-Directed Antiviral Research Center, Chonnam National University, Gwangju, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-6-phosphate aldolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
222Gilliamella apicolaMutation(s): 0 
Gene Names: A9G37_00305
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.818α = 90
b = 117.353β = 90
c = 204.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1A2C1009555

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release