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Yorodumi- EMDB-17777: Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17777 | ||||||||||||
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Title | Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA | ||||||||||||
Map data | main map | ||||||||||||
Sample |
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Keywords | glycolyl-CoA carboxylase / LIGASE | ||||||||||||
Function / homology | Function and homology information urea carboxylase activity / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / methylcrotonoyl-CoA carboxylase activity / lipid catabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Methylorubrum extorquens AM1 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.03 Å | ||||||||||||
Authors | Zarzycki J / Marchal DG / Schulz L / Prinz S / Erb TJ | ||||||||||||
Funding support | European Union, Germany, 3 items
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Citation | Journal: ACS Synth Biol / Year: 2023 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17777.map.gz | 180.1 MB | EMDB map data format | |
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Header (meta data) | emd-17777-v30.xml emd-17777.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17777_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_17777.png | 192.4 KB | ||
Filedesc metadata | emd-17777.cif.gz | 6.3 KB | ||
Others | emd_17777_half_map_1.map.gz emd_17777_half_map_2.map.gz | 322.4 MB 322.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17777 | HTTPS FTP |
-Validation report
Summary document | emd_17777_validation.pdf.gz | 880.3 KB | Display | EMDB validaton report |
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Full document | emd_17777_full_validation.pdf.gz | 879.8 KB | Display | |
Data in XML | emd_17777_validation.xml.gz | 24 KB | Display | |
Data in CIF | emd_17777_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17777 | HTTPS FTP |
-Related structure data
Related structure data | 8pn7MC 8pn8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17777.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_17777_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_17777_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : glycolyl-CoA carboxylase with bound CoA
Entire | Name: glycolyl-CoA carboxylase with bound CoA |
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Components |
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-Supramolecule #1: glycolyl-CoA carboxylase with bound CoA
Supramolecule | Name: glycolyl-CoA carboxylase with bound CoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Methylorubrum extorquens AM1 (bacteria) |
-Macromolecule #1: Propionyl-CoA carboxylase beta chain
Macromolecule | Name: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase |
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Source (natural) | Organism: Methylorubrum extorquens AM1 (bacteria) |
Molecular weight | Theoretical: 56.064066 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKDILEKLEE RRAQARLGGR EKRLEAQHKR GKLTARERIE LLLDHGSFEE FDMFVQHRST DFGMEKQKIP GDGVVTGWGT VNGRTVFLF SKDFTVFGGS SSEAHAAKIV KVQDMALKMR APIIGIFDAG GARIQEGVAA LGGHGEVFRR NVAASGVIPQ I SVIMGPCA ...String: MKDILEKLEE RRAQARLGGR EKRLEAQHKR GKLTARERIE LLLDHGSFEE FDMFVQHRST DFGMEKQKIP GDGVVTGWGT VNGRTVFLF SKDFTVFGGS SSEAHAAKIV KVQDMALKMR APIIGIFDAG GARIQEGVAA LGGHGEVFRR NVAASGVIPQ I SVIMGPCA GGDVYSPAMT DFIFMVRDTS YMFVTGPDVV KTVTNEVVTA EELGGAKVHT SKSSIADGSF ENDVEAILQI RR LLDFLPA NNIEGVPEIE SFDDVNRLDK SLDTLIPDNP NKPYDMGELI RRVVDEGDFF EIQAAYARNI ITGFGRVEGR TVG FVANQP LVLAGVLDSD ASRKAARFVR FCNAFSIPIV TFVDVPGFLP GTAQEYGGLI KHGAKLLFAY SQATVPLVTI ITRK AFGGA YIVMASKHVG ADLNYAWPTA QIAVMGAKGA VEIIFRAEIG DADKVAERTK EYEDRFLSPF VAAERGYIDE VIMPH STRK RIARALGMLR TKEMEQPRKK HDNIPL UniProtKB: Propionyl-CoA carboxylase beta chain |
-Macromolecule #2: Propionyl-CoA carboxylase alpha subunit
Macromolecule | Name: Propionyl-CoA carboxylase alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase |
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Source (natural) | Organism: Methylorubrum extorquens AM1 (bacteria) |
Molecular weight | Theoretical: 71.986961 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MFDKILIANR GEIACRIIKT AQKMGIKTVA VYSDADRDAV HVAMADEAVH IGPAPAAQSY LLIEKIIDAC KQTGAQAVHP GYGFLSERE SFPKALAEAG IVFIGPNPGA IAAMGDKIES KKAAAAAEVS TVPGFLGVIE SPEHAVTIAD EIGYPVMIKA S AGGGGKGM ...String: MFDKILIANR GEIACRIIKT AQKMGIKTVA VYSDADRDAV HVAMADEAVH IGPAPAAQSY LLIEKIIDAC KQTGAQAVHP GYGFLSERE SFPKALAEAG IVFIGPNPGA IAAMGDKIES KKAAAAAEVS TVPGFLGVIE SPEHAVTIAD EIGYPVMIKA S AGGGGKGM RIAESADEVA EGFARAKSEA SSSFGDDRVF VEKFITDPRH IEIQVIGDKH GNVIYLGERE CSIQRRNQKV IE EAPSPLL DEETRRKMGE QAVALAKAVN YDSAGTVEFV AGQDKSFYFL EMNTRLQVEH PVTEMITGLD LVELMIRVAA GEK LPLSQD QVKLDGWAVE SRVYAEDPTR NFLPSIGRLT TYQPPEEGPL GGAIVRNDTG VEEGGEIAIH YDPMIAKLVT WAPT RLEAI EAQATALDAF AIEGIRHNIP FLATLMAHPR WRDGRLSTGF IKEEFPEGFI APEPEGPVAH RLAAVAAAID HKLNI RKRG ISGQMRDPSL LTFQRERVVV LSGQRFNVTV DPDGDDLLVT FDDGTTAPVR SAWRPGAPVW SGTVGDQSVA IQVRPL LNG VFLQHAGAAA EARVFTRREA ELADLMPVKE NAGSGKQLLC PMPGLVKQIM VSEGQEVKNG EPLAIVEAMK MENVLRA ER DGTISKIAAK EGDSLAVDAV ILEFA UniProtKB: propionyl-CoA carboxylase |
-Macromolecule #3: COENZYME A
Macromolecule | Name: COENZYME A / type: ligand / ID: 3 / Number of copies: 6 / Formula: COA |
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Molecular weight | Theoretical: 767.534 Da |
Chemical component information | ChemComp-COA: |
-Macromolecule #4: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Macromolecule | Name: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL type: ligand / ID: 4 / Number of copies: 6 / Formula: BTI |
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Molecular weight | Theoretical: 228.311 Da |
Chemical component information | ChemComp-BTI: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 1476 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |