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- PDB-8ypz: Crystal strcture of human phosphoribosyl pyrophosphate synthetase... -

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Basic information

Entry
Database: PDB / ID: 8ypz
TitleCrystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP
ComponentsRibose-phosphate pyrophosphokinase 1
KeywordsBIOSYNTHETIC PROTEIN / Purine biosynthesis
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / 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 / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / 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 / cytoplasm / cytosol
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / GUANOSINE-5'-DIPHOSPHATE / 5-O-phosphono-alpha-D-ribofuranose / PHOSPHATE ION / Ribose-phosphate pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Nat Commun / Year: 2025
Title: PRPS2 enhances RNA m 6 A methylation by stimulating SAM synthesis through enzyme-dependent and independent mechanisms.
Authors: Zhang, L. / Zhao, X. / Hu, J. / Li, T. / Chen, H.Z. / Zhang, A. / Wang, H. / Yu, J. / Zhang, L.
History
DepositionMar 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose-phosphate pyrophosphokinase 1
B: Ribose-phosphate pyrophosphokinase 1
C: Ribose-phosphate pyrophosphokinase 1
D: Ribose-phosphate pyrophosphokinase 1
E: Ribose-phosphate pyrophosphokinase 1
F: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,42229
Polymers209,0116
Non-polymers7,41123
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33610 Å2
ΔGint-168 kcal/mol
Surface area59420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.876, 186.876, 160.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDEF

#1: Protein
Ribose-phosphate pyrophosphokinase 1 / PPRibP / Phosphoribosyl pyrophosphate synthase I / PRS-I


Mass: 34835.121 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: P60891, ribose-phosphate diphosphokinase
#3: Sugar
ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 81 molecules

#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium acetate, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 3→48.7 Å / Num. obs: 62270 / % possible obs: 100 % / Redundancy: 17.4 % / CC1/2: 0.764 / Net I/σ(I): 11.2
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 6340 / CC1/2: 0.764

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.17.1-3660refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H06

2h06


Resolution: 3→48.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.31 --
Rwork0.26 --
obs-62270 100 %
Displacement parametersBiso mean: 42.05 Å2
Refinement stepCycle: LAST / Resolution: 3→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14013 0 450 63 14526
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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