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Yorodumi- EMDB-38855: GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38855 | |||||||||
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Title | GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | L-proline biosynthesis / filamentous enzyme / TRANSFERASE / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / hyperosmotic salinity response / root development / L-proline biosynthetic process / proline biosynthetic process ...delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / hyperosmotic salinity response / root development / L-proline biosynthetic process / proline biosynthetic process / response to water deprivation / phosphorylation / response to salt stress / chloroplast / response to oxidative stress / Golgi apparatus / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang T / Guo CJ / Liu JL | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Plants / Year: 2024 Title: Dynamic Arabidopsis P5CS filament facilitates substrate channelling. Authors: Chen-Jun Guo / Tianyi Zhang / Qingqing Leng / Xian Zhou / Jiale Zhong / Ji-Long Liu / Abstract: In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing ...In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing the initial two-step conversion from glutamate to proline. Here we determine the first structure of plant P5CS. Our results show that Arabidopsis thaliana P5CS1 (AtP5CS1) and P5CS2 (AtP5CS2) can form enzymatic filaments in a substrate-sensitive manner. The destruction of AtP5CS filaments by mutagenesis leads to a significant reduction in enzymatic activity. Furthermore, separate activity tests on two domains reveal that filament-based substrate channelling is essential for maintaining the high catalytic efficiency of AtP5CS. Our study demonstrates the unique mechanism for the efficient catalysis of AtP5CS, shedding light on the intricate mechanisms underlying plant proline metabolism and stress response. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38855.map.gz | 26.3 MB | EMDB map data format | |
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Header (meta data) | emd-38855-v30.xml emd-38855.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38855_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_38855.png | 91.1 KB | ||
Masks | emd_38855_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-38855.cif.gz | 5.9 KB | ||
Others | emd_38855_half_map_1.map.gz emd_38855_half_map_2.map.gz | 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38855 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38855 | HTTPS FTP |
-Validation report
Summary document | emd_38855_validation.pdf.gz | 822.4 KB | Display | EMDB validaton report |
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Full document | emd_38855_full_validation.pdf.gz | 821.9 KB | Display | |
Data in XML | emd_38855_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_38855_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38855 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38855 | HTTPS FTP |
-Related structure data
Related structure data | 8y2hMC 8j0fC C: citing same article (ref.) M: atomic model generated by this map |
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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_38855.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38855_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38855_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38855_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Arabidopsis thaliana P5CSA incubated with all substrates.
Entire | Name: Arabidopsis thaliana P5CSA incubated with all substrates. |
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Components |
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-Supramolecule #1: Arabidopsis thaliana P5CSA incubated with all substrates.
Supramolecule | Name: Arabidopsis thaliana P5CSA incubated with all substrates. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 78.9 kDa/nm |
-Macromolecule #1: Delta-1-pyrroline-5-carboxylate synthase A
Macromolecule | Name: Delta-1-pyrroline-5-carboxylate synthase A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 78.993086 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH MEELDRSRAF ARDVKRIVVK VGTAVVTGKG GRLALGRLGA LCEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSS FADLQKPQTE LDGKACAGVG QSSLMAYYET MFDQLDVTAA QLLVNDSSFR DKDFRKQLNE TVKSMLDLRV I PIFNENDA ...String: MGSSHHHHHH MEELDRSRAF ARDVKRIVVK VGTAVVTGKG GRLALGRLGA LCEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSS FADLQKPQTE LDGKACAGVG QSSLMAYYET MFDQLDVTAA QLLVNDSSFR DKDFRKQLNE TVKSMLDLRV I PIFNENDA ISTRRAPYQD SSGIFWDNDS LAALLALELK ADLLILLSDV EGLYTGPPSD PNSKLIHTFV KEKHQDEITF GD KSRLGRG GMTAKVKAAV NAAYAGIPVI ITSGYSAENI DKVLRGLRVG TLFHQDARLW APITDSNARD MAVAARESSR KLQ ALSSED RKKILLDIAD ALEANVTTIK AENELDVASA QEAGLEESMV ARLVMTPGKI SSLAASVRKL ADMEDPIGRV LKKT EVADG LVLEKTSSPL GVLLIVFESR PDALVQIASL AIRSGNGLLL KGGKEARRSN AILHKVITDA IPETVGGKLI GLVTS REEI PDLLKLDDVI DLVIPRGSNK LVTQIKNTTK IPVLGHADGI CHVYVDKACD TDMAKRIVSD AKLDYPAACN AMETLL VHK DLEQNAVLNE LIFALQSNGV TLYGGPRASK ILNIPEARSF NHEYCAKACT VEVVEDVYGA IDHIHRHGSA HTDCIVT ED HEVAELFLRQ VDSAAVFHNA STRFSDGFRF GLGAEVGVST GRIHARGPVG VEGLLTTRWI MRGKGQVVDG DNGIVYTH Q DIPIQA UniProtKB: Delta-1-pyrroline-5-carboxylate synthase A |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |