[English] 日本語
![](img/lk-miru.gif)
- PDB-8pn8: Engineered glycolyl-CoA carboxylase (L100N variant) with bound CoA -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8pn8 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Engineered glycolyl-CoA carboxylase (L100N variant) with bound CoA | ||||||||||||
![]() |
| ||||||||||||
![]() | LIGASE / glycolyl-CoA carboxylase | ||||||||||||
Function / homology | ![]() propionyl-CoA carboxylase / urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / lipid catabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 Å | ||||||||||||
![]() | Zarzycki, J. / Marchal, D.G. / Schulz, L. / Prinz, S. / Erb, T.J. | ||||||||||||
Funding support | European Union, ![]()
| ||||||||||||
![]() | ![]() Title: Machine Learning-Supported Enzyme Engineering toward Improved CO-Fixation of Glycolyl-CoA Carboxylase. Authors: Daniel G Marchal / Luca Schulz / Ingmar Schuster / Jelena Ivanovska / Nicole Paczia / Simone Prinz / Jan Zarzycki / Tobias J Erb / ![]() Abstract: Glycolyl-CoA carboxylase (GCC) is a new-to-nature enzyme that catalyzes the key reaction in the tartronyl-CoA (TaCo) pathway, a synthetic photorespiration bypass that was recently designed to improve ...Glycolyl-CoA carboxylase (GCC) is a new-to-nature enzyme that catalyzes the key reaction in the tartronyl-CoA (TaCo) pathway, a synthetic photorespiration bypass that was recently designed to improve photosynthetic CO fixation. GCC was created from propionyl-CoA carboxylase (PCC) through five mutations. However, despite reaching activities of naturally evolved biotin-dependent carboxylases, the quintuple substitution variant GCC M5 still lags behind 4-fold in catalytic efficiency compared to its template PCC and suffers from futile ATP hydrolysis during CO fixation. To further improve upon GCC M5, we developed a machine learning-supported workflow that reduces screening efforts for identifying improved enzymes. Using this workflow, we present two novel GCC variants with 2-fold increased carboxylation rate and 60% reduced energy demand, respectively, which are able to address kinetic and thermodynamic limitations of the TaCo pathway. Our work highlights the potential of combining machine learning and directed evolution strategies to reduce screening efforts in enzyme engineering. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 851.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 693 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 124.9 KB | Display | |
Data in CIF | ![]() | 189.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17778MC ![]() 8pn7C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 55990.953 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pccB, MexAM1_META1p0172 / Production host: ![]() ![]() #2: Protein | Mass: 71986.961 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pccA, MexAM1_META1p3203 / Production host: ![]() ![]() #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-BTI / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: glycolyl-CoA carboxylase with bound CoA / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: D3 (2x3 fold dihedral) |
3D reconstruction | Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113824 / Symmetry type: POINT |