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- EMDB-27284: Human PRPS1 with Phosphate and ATP; Filament Interface -

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Basic information

Entry
Database: EMDB / ID: EMD-27284
TitleHuman PRPS1 with Phosphate and ATP; Filament Interface
Map dataHuman PRPS1 with Phosphate and ATP; Interface Centered
Sample
  • Complex: Filament interface of phosphoribosyl pyrophosphate synthetase 1 with phosphate and ATP
    • Protein or peptide: Ribose-phosphate pyrophosphokinase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsphosphoribosyl pyrophosphate synthetase / ATP substrate / TRANSFERASE
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribonucleoside monophosphate biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process ...5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribonucleoside monophosphate biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / kinase activity / nervous system development / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
Ribose-phosphate pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsHvorecny KL / Kollman JM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI145111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118396 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Human PRPS1 filaments stabilize allosteric sites to regulate activity.
Authors: Kelli L Hvorecny / Kenzee Hargett / Joel D Quispe / Justin M Kollman /
Abstract: The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and ...The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and mutations in the human enzyme PRPS1 lead to a spectrum of diseases. Here we determine structures of human PRPS1 filaments in active and inhibited states, with fixed assembly contacts accommodating both conformations. The conserved assembly interface stabilizes the binding site for the essential activator phosphate, increasing activity in the filament. Some disease mutations alter assembly, supporting the link between filament stability and activity. Structures of active PRPS1 filaments turning over substrate also reveal coupling of catalysis in one active site with product release in an adjacent site. PRPS1 filaments therefore provide an additional layer of allosteric control, conserved throughout evolution, with likely impact on metabolic homeostasis. Stabilization of allosteric binding sites by polymerization adds to the growing diversity of assembly-based enzyme regulatory mechanisms.
History
DepositionJun 14, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27284.png

Downloads & links

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Map

FileDownload / File: emd_27284.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman PRPS1 with Phosphate and ATP; Interface Centered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25
Minimum - Maximum-6.657324 - 16.051960000000001
Average (Standard dev.)0.000000000000315 (±0.3972447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human PRPS1 with Phosphate and ATP; Interface Centered half 1

Fileemd_27284_half_map_1.map
AnnotationHuman PRPS1 with Phosphate and ATP; Interface Centered half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human PRPS1 with Phosphate and ATP; Interface Centered half 2

Fileemd_27284_half_map_2.map
AnnotationHuman PRPS1 with Phosphate and ATP; Interface Centered half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament interface of phosphoribosyl pyrophosphate synthetase 1 w...

EntireName: Filament interface of phosphoribosyl pyrophosphate synthetase 1 with phosphate and ATP
Components
  • Complex: Filament interface of phosphoribosyl pyrophosphate synthetase 1 with phosphate and ATP
    • Protein or peptide: Ribose-phosphate pyrophosphokinase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Filament interface of phosphoribosyl pyrophosphate synthetase 1 w...

SupramoleculeName: Filament interface of phosphoribosyl pyrophosphate synthetase 1 with phosphate and ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Six copies of PRPS1 assemble to form a hexamer; hexamers assembly linearly to form filaments.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ribose-phosphate pyrophosphokinase 1

MacromoleculeName: Ribose-phosphate pyrophosphokinase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ribose-phosphate diphosphokinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.835121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLMEL LIMINACKIA SASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLKWIRENI S EWRNCTIV ...String:
SPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLMEL LIMINACKIA SASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA GADHIITMDL HASQIQGFFD IPVDNLYAEP AVLKWIRENI S EWRNCTIV SPDAGGAKRV TSIADRLNVD FALIHKERKK ANEVDRMVLV GDVKDRVAIL VDDMADTCGT ICHAADKLLS AG ATRVYAI LTHGIFSGPA ISRINNACFE AVVVTNTIPQ EDKMKHCSKI QVIDISMILA EAIRRTHNGE SVSYLFSHVP L

UniProtKB: Ribose-phosphate pyrophosphokinase 1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 24 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.6
GridModel: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PHENIX (ver. 1.18) / Number images used: 155577
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8dbh:
Human PRPS1 with Phosphate and ATP; Filament Interface

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