Crystal structure of Escherichia coli glyoxylate carboligase double mutant in complex with glycolaldehyde

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 

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Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose.

Kim, J.H.Cheon, H.Jo, H.J.Kim, J.W.Kim, G.Y.Seo, H.R.Seo, P.W.Kim, J.S.Park, J.B.

(2023) Int J Biol Macromol 253: 127674-127674

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.127674
  • Primary Citation of Related Structures:  
    8I01, 8I05, 8I07, 8I08

  • PubMed Abstract: 

    A number of carboligases, which catalyze condensation of C1- and/or C2-aldehydes into multi-carbon products, have been reported. However, their catalytic activities and/or regioselectivities remained rather low. Thereby, this study has focused on engineering of C1 and C2 carboligases for the regioselective condensation of C1-formaldehyde into C4-erythrulose via C2-glycolaldehyde. The crystal structure of the glyoxylate carboligase from Escherichia coli (EcGCL) was elucidated in complex with glycolaldehyde. A structure-guided rationale generated several mutants, one of whose catalytic activity reached 15.6 M -1 ·s -1 , almost 10 times greater than the wild-type enzyme. Another variant (i.e., EcGCL _R484M/N283Q/L478M/M488L/R284K ) has shown significantly increased stability to the glycolaldehyde toxicity, enabling production of glycolaldehyde to 31 mM from 75 mM formaldehyde (conversion: 83 %). Besides, the E1 subunit of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus (VvSucA) was engineered as a regiospecific C2 carboligase for condensation of glycolaldehyde into erythrulose. The combination of EcGCL _R484M/N283Q/L478M/M488L/R284K and VvSucA _K228L led to the cascade production of erythrulose to 8 mM from 90 mM formaldehyde via glycolaldehyde without byproduct formation. This study will contribute to valorization of C1 gases into industrially relevant multi-carbon products in an environment-friendly way.

  • Organizational Affiliation

    Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyoxylate carboligase
A, B, C, D, E
A, B, C, D, E, F
594Escherichia coli K-12Mutation(s): 2 
Gene Names: gclb0507JW0495
Find proteins for P0AEP7 (Escherichia coli (strain K12))
Explore P0AEP7 
Go to UniProtKB:  P0AEP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEP7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
DA [auth D]
I [auth A]
KA [auth E]
P [auth B]
QA [auth F]
DA [auth D],
I [auth A],
KA [auth E],
P [auth B],
QA [auth F],
V [auth C]
C27 H33 N9 O15 P2
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
EA [auth D]
J [auth A]
LA [auth E]
Q [auth B]
RA [auth F]
EA [auth D],
J [auth A],
LA [auth E],
Q [auth B],
RA [auth F],
W [auth C]
C12 H19 N4 O7 P2 S
UQ1 (Subject of Investigation/LOI)
Query on UQ1

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
HA [auth D]
IA [auth D]
L [auth A]
AA [auth C],
BA [auth C],
HA [auth D],
IA [auth D],
L [auth A],
M [auth A],
MA [auth E],
NA [auth E],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F]
C14 H18 O4
DW3 (Subject of Investigation/LOI)
Query on DW3

Download Ideal Coordinates CCD File 
FA [auth D]
GA [auth D]
K [auth A]
R [auth B]
X [auth C]
FA [auth D],
GA [auth D],
K [auth A],
R [auth B],
X [auth C],
Y [auth C]
C2 H4 O2
MG (Subject of Investigation/LOI)
Query on MG

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CA [auth D]
G [auth A]
H [auth A]
JA [auth E]
N [auth B]
CA [auth D],
G [auth A],
H [auth A],
JA [auth E],
N [auth B],
O [auth B],
OA [auth F],
PA [auth F],
U [auth C],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.299α = 90
b = 189.299β = 90
c = 246.982γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references