+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33883 | |||||||||
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Title | Structural basis of human PRPS2 filaments | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phosphoribosylpyrophosphate synthetase / complex / filament / TRANSFERASE | |||||||||
Function / homology | Function and homology information 5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / pentose-phosphate shunt / purine nucleotide biosynthetic process / nucleobase-containing compound metabolic process / kinase activity ...5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / 5-phosphoribose 1-diphosphate biosynthetic process / pentose-phosphate shunt / purine nucleotide biosynthetic process / nucleobase-containing compound metabolic process / kinase activity / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Lu GM / Hu HH / Liu JL | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Biosci / Year: 2023 Title: Structural basis of human PRPS2 filaments. Authors: Guang-Ming Lu / Huan-Huan Hu / Chia-Chun Chang / Jiale Zhong / Xian Zhou / Chen-Jun Guo / Tianyi Zhang / Yi-Lan Li / Boqi Yin / Ji-Long Liu / Abstract: BACKGROUND: PRPP synthase (PRPS) transfers the pyrophosphate groups from ATP to ribose-5-phosphate to produce 5-phosphate ribose-1-pyrophosphate (PRPP), a key intermediate in the biosynthesis of ...BACKGROUND: PRPP synthase (PRPS) transfers the pyrophosphate groups from ATP to ribose-5-phosphate to produce 5-phosphate ribose-1-pyrophosphate (PRPP), a key intermediate in the biosynthesis of several metabolites including nucleotides, dinucleotides and some amino acids. There are three PRPS isoforms encoded in human genome. While human PRPS1 (hPRPS1) and human PRPS2 (hPRPS2) are expressed in most tissues, human PRPS3 (hPRPS3) is exclusively expressed in testis. Although hPRPS1 and hPRPS2 share 95% sequence identity, hPRPS2 has been shown to be less sensitive to allosteric inhibition and specifically upregulated in certain cancers in the translational level. Recent studies demonstrate that PRPS can form a subcellular compartment termed the cytoophidium in multiple organisms across prokaryotes and eukaryotes. Forming filaments and cytoophidia is considered as a distinctive mechanism involving the polymerization of the protein. Previously we solved the filament structures of Escherichia coli PRPS (ecPRPS) using cryo-electron microscopy (cryo-EM) . RESULTS: Order to investigate the function and molecular mechanism of hPRPS2 polymerization, here we solve the polymer structure of hPRPS2 at 3.08 Å resolution. hPRPS2 hexamers stack into polymers ...RESULTS: Order to investigate the function and molecular mechanism of hPRPS2 polymerization, here we solve the polymer structure of hPRPS2 at 3.08 Å resolution. hPRPS2 hexamers stack into polymers in the conditions with the allosteric/competitive inhibitor ADP. The binding modes of ADP at the canonical allosteric site and at the catalytic active site are clearly determined. A point mutation disrupting the inter-hexamer interaction prevents hPRPS2 polymerization and results in significantly reduced catalytic activity. CONCLUSION: Findings suggest that the regulation of hPRPS2 polymer is distinct from ecPRPS polymer and provide new insights to the regulation of hPRPS2 with structural basis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33883.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-33883-v30.xml emd-33883.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33883_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_33883.png | 63.1 KB | ||
Masks | emd_33883_msk_1.map | 64 MB | Mask map | |
Others | emd_33883_half_map_1.map.gz emd_33883_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33883 | HTTPS FTP |
-Related structure data
Related structure data | 7yk1MC 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_33883.map.gz / Format: CCP4 / Size: 64 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_33883_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33883_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33883_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Filament structure of human phosphoribosylpyrophosphate synthetase2.
Entire | Name: Filament structure of human phosphoribosylpyrophosphate synthetase2. |
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Components |
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-Supramolecule #1: Filament structure of human phosphoribosylpyrophosphate synthetase2.
Supramolecule | Name: Filament structure of human phosphoribosylpyrophosphate synthetase2. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ribose-phosphate pyrophosphokinase 2
Macromolecule | Name: Ribose-phosphate pyrophosphokinase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: ribose-phosphate diphosphokinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.640969 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MPNIVLFSGS SHQDLSQRVA DRLGLELGKV VTKKFSNQET SVEIGESVRG EDVYIIQSGC GEINDNLMEL LIMINACKIA SSSRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLQWIRENI A EWKNCIIV ...String: MPNIVLFSGS SHQDLSQRVA DRLGLELGKV VTKKFSNQET SVEIGESVRG EDVYIIQSGC GEINDNLMEL LIMINACKIA SSSRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLQWIRENI A EWKNCIIV SPDAGGAKRV TSIADRLNVE FALIHKERKK ANEVDRMVLV GDVKDRVAIL VDDMADTCGT ICHAADKLLS AG ATKVYAI LTHGIFSGPA ISRINNAAFE AVVVTNTIPQ EDKMKHCTKI QVIDISMILA EAIRRTHNGE SVSYLFSHVP LHH HHHH UniProtKB: Ribose-phosphate pyrophosphokinase 2 |
-Macromolecule #2: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2403 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |