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- PDB-8yq0: Crystal structure of human phosphoribosyl pyrophosphate synthetas... -

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Basic information

Entry
Database: PDB / ID: 8yq0
TitleCrystal structure of human phosphoribosyl pyrophosphate synthetase 1(PRPS1) chimera swapped with three residues from PRPS2
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 / 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
5-O-phosphono-alpha-D-ribofuranose / Ribose-phosphate pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
G: Ribose-phosphate pyrophosphokinase 1
H: Ribose-phosphate pyrophosphokinase 1
I: Ribose-phosphate pyrophosphokinase 1
J: Ribose-phosphate pyrophosphokinase 1
K: Ribose-phosphate pyrophosphokinase 1
L: Ribose-phosphate pyrophosphokinase 1
M: Ribose-phosphate pyrophosphokinase 1
N: Ribose-phosphate pyrophosphokinase 1
O: Ribose-phosphate pyrophosphokinase 1
P: Ribose-phosphate pyrophosphokinase 1
Q: Ribose-phosphate pyrophosphokinase 1
R: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,85821
Polymers632,16818
Non-polymers6903
Water00
1
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)211,1838
Polymers210,7236
Non-polymers4602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-107 kcal/mol
Surface area66660 Å2
MethodPISA
2
G: Ribose-phosphate pyrophosphokinase 1
H: Ribose-phosphate pyrophosphokinase 1
I: Ribose-phosphate pyrophosphokinase 1
J: Ribose-phosphate pyrophosphokinase 1
K: Ribose-phosphate pyrophosphokinase 1
L: Ribose-phosphate pyrophosphokinase 1


Theoretical massNumber of molelcules
Total (without water)210,7236
Polymers210,7236
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22330 Å2
ΔGint-102 kcal/mol
Surface area65300 Å2
MethodPISA
3
M: Ribose-phosphate pyrophosphokinase 1
N: Ribose-phosphate pyrophosphokinase 1
O: Ribose-phosphate pyrophosphokinase 1
P: Ribose-phosphate pyrophosphokinase 1
Q: Ribose-phosphate pyrophosphokinase 1
R: Ribose-phosphate pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,9537
Polymers210,7236
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22120 Å2
ΔGint-104 kcal/mol
Surface area65580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.083, 108.083, 659.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 35120.418 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: human phosphoribosyl pyrophosphate synthetase 1(PRPS1) chimera swapped with three residues (VGE) from PRPS2_HUMAN.
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: P60891, ribose-phosphate diphosphokinase
#2: 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.: 3 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Lithium sulfate, 20% 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: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 3.1→50.01 Å / Num. obs: 135705 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.538 / Rpim(I) all: 0.153 / Rrim(I) all: 0.559 / Χ2: 1.048 / Net I/σ(I): 2.2
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 13496 / CC1/2: 0.645

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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: 3.1→50.01 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 6684 4.99 %
Rwork0.196 --
obs0.199 133985 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.57 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42181 0 42 0 42223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242793
X-RAY DIFFRACTIONf_angle_d1.71157885
X-RAY DIFFRACTIONf_dihedral_angle_d10.7326817
X-RAY DIFFRACTIONf_chiral_restr0.0966904
X-RAY DIFFRACTIONf_plane_restr0.0127421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A24435X-RAY DIFFRACTIONPOSITIONAL
12B24435X-RAY DIFFRACTIONPOSITIONAL
13C24435X-RAY DIFFRACTIONPOSITIONAL
14D24435X-RAY DIFFRACTIONPOSITIONAL
15E24435X-RAY DIFFRACTIONPOSITIONAL
16F24435X-RAY DIFFRACTIONPOSITIONAL
17G24435X-RAY DIFFRACTIONPOSITIONAL
18H24435X-RAY DIFFRACTIONPOSITIONAL
19I24435X-RAY DIFFRACTIONPOSITIONAL
110J24435X-RAY DIFFRACTIONPOSITIONAL
111K24435X-RAY DIFFRACTIONPOSITIONAL
112L24435X-RAY DIFFRACTIONPOSITIONAL
113M24435X-RAY DIFFRACTIONPOSITIONAL
114N24435X-RAY DIFFRACTIONPOSITIONAL
115O24435X-RAY DIFFRACTIONPOSITIONAL
116P24435X-RAY DIFFRACTIONPOSITIONAL
117Q24435X-RAY DIFFRACTIONPOSITIONAL
118R24435X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1014-3.13660.35481830.3063788X-RAY DIFFRACTION88
3.1366-3.17350.33162450.3054091X-RAY DIFFRACTION95
3.1735-3.21220.35512380.3044072X-RAY DIFFRACTION97
3.2122-3.25290.35492470.29594247X-RAY DIFFRACTION98
3.2529-3.29570.40352070.2884212X-RAY DIFFRACTION99
3.2957-3.34080.33912290.29924201X-RAY DIFFRACTION99
3.3408-3.38850.37922170.28924362X-RAY DIFFRACTION99
3.3885-3.43910.36752270.27584173X-RAY DIFFRACTION99
3.4391-3.49280.32592410.26534314X-RAY DIFFRACTION99
3.4928-3.55010.35382220.25474221X-RAY DIFFRACTION99
3.5501-3.61130.26722170.23594322X-RAY DIFFRACTION99
3.6113-3.67690.29052030.23044265X-RAY DIFFRACTION100
3.6769-3.74760.27852420.23024268X-RAY DIFFRACTION100
3.7476-3.82410.27432670.22274234X-RAY DIFFRACTION100
3.8241-3.90720.29022190.21194266X-RAY DIFFRACTION100
3.9072-3.99810.26211960.21184315X-RAY DIFFRACTION99
3.9981-4.0980.27012200.19214258X-RAY DIFFRACTION100
4.098-4.20870.22112430.17534245X-RAY DIFFRACTION100
4.2087-4.33250.22172080.16814349X-RAY DIFFRACTION100
4.3325-4.47230.21972000.15464311X-RAY DIFFRACTION100
4.4723-4.6320.21332510.15974241X-RAY DIFFRACTION100
4.632-4.81730.2162430.15374239X-RAY DIFFRACTION100
4.8173-5.03640.19852210.1524271X-RAY DIFFRACTION100
5.0364-5.30160.23322010.15694322X-RAY DIFFRACTION100
5.3016-5.63340.23661870.17934351X-RAY DIFFRACTION100
5.6334-6.06770.25742210.1854263X-RAY DIFFRACTION100
6.0677-6.6770.23141890.18374339X-RAY DIFFRACTION100
6.677-7.64020.22942440.17164301X-RAY DIFFRACTION100
7.6402-9.61470.15162380.12294267X-RAY DIFFRACTION100
9.6147-50.0090.17612180.16414193X-RAY DIFFRACTION97

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