8I05 | pdb_00008i05

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 398.78 kDa 
  • Atom Count: 30,124 
  • Modeled Residue Count: 3,564 
  • Deposited Residue Count: 3,564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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))
Explore P0AEP7 
Go to UniProtKB:  P0AEP7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEP7
Sequence Annotations
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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 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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