8I05

Crystal structure of Escherichia coli glyoxylate carboligase double mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 4.1.1.47
UniProt
Find proteins for P0AEP7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]
GA [auth E]
KA [auth F]
M [auth B]
S [auth C]
G [auth A],
GA [auth E],
KA [auth F],
M [auth B],
S [auth C],
Z [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
AA [auth D]
H [auth A]
HA [auth E]
LA [auth F]
N [auth B]
AA [auth D],
H [auth A],
HA [auth E],
LA [auth F],
N [auth B],
T [auth C]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
UQ0 (Subject of Investigation/LOI)
Query on UQ0

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
JA [auth E]
K [auth A]
DA [auth D],
EA [auth D],
FA [auth D],
JA [auth E],
K [auth A],
L [auth A],
NA [auth F],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C]
2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE
C9 H10 O4
UIXPTCZPFCVOQF-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
I [auth A]
IA [auth E]
J [auth A]
BA [auth D],
CA [auth D],
I [auth A],
IA [auth E],
J [auth A],
MA [auth F],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.172α = 90
b = 189.172β = 90
c = 246.506γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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