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- EMDB-33306: E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/A... -
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Open data
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Basic information
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Title | E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P | |||||||||
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![]() | Allosteric enzyme / Kinase / Transferase / Nucleotide biosynthesis / ATP-binding / Magnesium / Manganese / Metal-binding / Nucleotide-binding / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / protein hexamerization / phosphate ion binding / ADP binding / kinase activity ...ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / protein hexamerization / phosphate ion binding / ADP binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Hu HH / Lu GM / Chang CC / Liu JL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Filamentation modulates allosteric regulation of PRPS. Authors: Huan-Huan Hu / Guang-Ming Lu / Chia-Chun Chang / Yilan Li / Jiale Zhong / Chen-Jun Guo / Xian Zhou / Boqi Yin / Tianyi Zhang / Ji-Long Liu / ![]() ![]() Abstract: Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP ...Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 40.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 87.6 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 956.2 KB | Display | ![]() |
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Full document | ![]() | 955.8 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xmvMC ![]() 7xmuC ![]() 7xn3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Density Histograms |
-Half map: #1
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-Half map: #2
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Density Histograms |
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Sample components
-Entire : E.coli PRPP syhthetase filament structure complex with ADP,AMP, M...
Entire | Name: E.coli PRPP syhthetase filament structure complex with ADP,AMP, Mg2+ and R5P |
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Components |
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-Supramolecule #1: E.coli PRPP syhthetase filament structure complex with ADP,AMP, M...
Supramolecule | Name: E.coli PRPP syhthetase filament structure complex with ADP,AMP, Mg2+ and R5P type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: a new allosteric for AMP binding |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ribose-phosphate pyrophosphokinase
Macromolecule | Name: Ribose-phosphate pyrophosphokinase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: ribose-phosphate diphosphokinase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.08409 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPDMKLFAGN ATPELAQRIA NRLYTSLGDA AVGRFSDGEV SVQINENVRG GDIFIIQSTC APTNDNLMEL VVMVDALRRA SAGRITAVI PYFGYARQDR RVRSARVPIT AKVVADFLSS VGVDRVLTVD LHAEQIQGFF DVPVDNVFGS PILLEDMLQL N LDNPIVVS ...String: MPDMKLFAGN ATPELAQRIA NRLYTSLGDA AVGRFSDGEV SVQINENVRG GDIFIIQSTC APTNDNLMEL VVMVDALRRA SAGRITAVI PYFGYARQDR RVRSARVPIT AKVVADFLSS VGVDRVLTVD LHAEQIQGFF DVPVDNVFGS PILLEDMLQL N LDNPIVVS PDIGGVVRAR AIAKLLNDTD MAIIDKRRPR ANVSQVMHII GDVAGRDCVL VDDMIDTGGT LCKAAEALKE RG AKRVFAY ATHPIFSGNA ANNLRNSVID EVVVCDTIPL SDEIKSLPNV RTLTLSGMLA EAIRRISNEE SISAMFEHHH HHH H UniProtKB: Ribose-phosphate pyrophosphokinase |
-Macromolecule #2: 5-O-phosphono-alpha-D-ribofuranose
Macromolecule | Name: 5-O-phosphono-alpha-D-ribofuranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: HSX |
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Molecular weight | Theoretical: 230.11 Da |
Chemical component information | ![]() ChemComp-HSX: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / 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: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #5: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ![]() ChemComp-AMP: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 810 / 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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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blot for 3.5 seconds with blot force of -1 before plunge-freezing. |
Details | The purifide monomer or oligomer protein was incubated with ADP,AMP and MgCl2 to form this type A(AMP/ADP) filament. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2566 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |