8I07

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted TPPClick on this verticalbar to view detailsBest fitted UQ1Click on this verticalbar to view detailsBest fitted DW3Click on this verticalbar to view details

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
594Escherichia coli K-12Mutation(s): 2 
Gene Names: gclb0507JW0495
EC: 4.1.1.47
UniProt
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
Expand
  • 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]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
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]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
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]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
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]
2-oxidanylethanal
C2 H4 O2
WGCNASOHLSPBMP-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth D]
G [auth A]
H [auth A]
JA [auth E]
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
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
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted TPPClick on this verticalbar to view detailsBest fitted UQ1Click on this verticalbar to view detailsBest fitted DW3Click on this verticalbar to view details

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