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- PDB-8ypy: Crystal strcuture of human phosphoribosyl pyrophosphate synthetas... -

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Basic information

Entry
Database: PDB / ID: 8ypy
TitleCrystal strcuture of human phosphoribosyl pyrophosphate synthetase2 (PRPS2) in complex with ligands
ComponentsIsoform 2 of Ribose-phosphate pyrophosphokinase 2
KeywordsBIOSYNTHETIC PROTEIN / purine biosynthesis
Function / homology
Function and homology information


5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / 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 ...5-Phosphoribose 1-diphosphate biosynthesis / ribonucleoside monophosphate biosynthetic process / 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 / 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 / : / 5-O-phosphono-alpha-D-ribofuranose / PHOSPHATE ION / Ribose-phosphate pyrophosphokinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
B: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
C: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
D: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
E: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
F: Isoform 2 of Ribose-phosphate pyrophosphokinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,88129
Polymers210,3206
Non-polymers5,56123
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29180 Å2
ΔGint-194 kcal/mol
Surface area64150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.701, 73.598, 170.500
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Isoform 2 of Ribose-phosphate pyrophosphokinase 2 / PPRibP / Phosphoribosyl pyrophosphate synthase II / PRS-II


Mass: 35053.277 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS2 / Production host: Escherichia coli (E. coli)
References: UniProt: P11908, 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.: 6 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 208 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium sulfate, 35% MPD

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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: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 2.74→46.91 Å / Num. obs: 54437 / % possible obs: 94.1 % / Redundancy: 4.2 % / CC1/2: 0.689 / Net I/σ(I): 9.6
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 2202 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H06

2h06


Resolution: 2.74→46.91 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 2789 5.12 %
Rwork0.272 --
obs0.273 54437 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.27 Å2
Refinement stepCycle: LAST / Resolution: 2.74→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13730 0 301 191 14222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02514217
X-RAY DIFFRACTIONf_angle_d2.34519297
X-RAY DIFFRACTIONf_dihedral_angle_d26.855499
X-RAY DIFFRACTIONf_chiral_restr0.1712332
X-RAY DIFFRACTIONf_plane_restr0.0132427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7413-2.78850.3542820.32271355X-RAY DIFFRACTION47
2.7885-2.83920.4154800.31371639X-RAY DIFFRACTION56
2.8392-2.89380.3549960.32571824X-RAY DIFFRACTION63
2.8938-2.95290.33091110.29622050X-RAY DIFFRACTION70
2.9529-3.01710.30041120.30042187X-RAY DIFFRACTION75
3.0171-3.08720.31531190.30072383X-RAY DIFFRACTION81
3.0872-3.16440.30241340.30242533X-RAY DIFFRACTION87
3.1644-3.250.36051320.31012695X-RAY DIFFRACTION92
3.25-3.34560.32961590.30122760X-RAY DIFFRACTION95
3.3456-3.45350.33181250.29382870X-RAY DIFFRACTION98
3.4535-3.57690.29581760.28512880X-RAY DIFFRACTION99
3.5769-3.72010.30821540.27522957X-RAY DIFFRACTION100
3.7201-3.88930.2831700.27142918X-RAY DIFFRACTION100
3.8893-4.09430.3011690.24792933X-RAY DIFFRACTION100
4.0943-4.35060.24961670.24922884X-RAY DIFFRACTION100
4.3506-4.68620.24381860.242912X-RAY DIFFRACTION100
4.6862-5.15730.26861470.23492966X-RAY DIFFRACTION100
5.1573-5.90230.27521540.28282953X-RAY DIFFRACTION100
5.9023-7.43150.31490.28743001X-RAY DIFFRACTION100
7.4315-46.9070.241670.2472948X-RAY DIFFRACTION97

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