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- PDB-7fha: Crystal structure of the ATP sulfurylase domain of human PAPSS2 i... -

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Basic information

Entry
Database: PDB / ID: 7fha
TitleCrystal structure of the ATP sulfurylase domain of human PAPSS2 in complex with APS
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
KeywordsBIOSYNTHETIC PROTEIN / ATP sulfurylase
Function / homology
Function and homology information


Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process ...Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process / nucleotidyltransferase activity / bone development / blood coagulation / ATP binding / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / beta-D-glucopyranose / : / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, P. / Zhang, L. / Zhang, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853118 China
National Natural Science Foundation of China (NSFC)22077081 China
National Natural Science Foundation of China (NSFC)21722802 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural basis for the substrate recognition mechanism of ATP-sulfurylase domain of human PAPS synthase 2.
Authors: Zhang, P. / Zhang, L. / Hou, Z. / Lin, H. / Gao, H. / Zhang, L.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,52310
Polymers90,0382
Non-polymers1,4858
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-38 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.111, 131.105, 135.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 / PAPS synthase 2 / PAPSS 2 / Sulfurylase kinase 2 / SK 2 / SK2


Mass: 45018.793 Da / Num. of mol.: 2 / Fragment: Sulfate adenylyltransferase,ATP sulfurylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS2, ATPSK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95340, sulfate adenylyltransferase, adenylyl-sulfate kinase
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 858 molecules

#2: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O10PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.1M HEPES, pH7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 75483 / % possible obs: 99.66 % / Redundancy: 12.6 % / CC1/2: 0.973 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 7394 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X6V

1x6v


Resolution: 2→47.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 3881 5.14 %
Rwork0.1519 71602 -
obs0.1535 75483 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.42 Å2 / Biso mean: 27.7116 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 2→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 90 852 7226
Biso mean--29.41 35.33 -
Num. residues----781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.22761240.17752321244592
2.02-2.050.2271280.172725522680100
2.05-2.080.23041220.174725482670100
2.08-2.110.22521340.169424932627100
2.11-2.140.20281500.163925552705100
2.14-2.170.1981230.159225062629100
2.17-2.20.21881120.162125782690100
2.2-2.240.20491330.162725322665100
2.24-2.280.19081360.15525342670100
2.28-2.320.17141330.154125402673100
2.32-2.360.20461530.159125322685100
2.36-2.410.19451510.156825372688100
2.41-2.460.19691440.159925472691100
2.46-2.520.17451390.158725482687100
2.52-2.580.21161440.160525602704100
2.58-2.650.17921580.157425032661100
2.65-2.730.17451550.159125412696100
2.73-2.820.18611410.160625722713100
2.82-2.920.19851420.166425372679100
2.92-3.040.20011300.162325722702100
3.04-3.170.18511540.162725592713100
3.18-3.340.19821370.162825672704100
3.34-3.550.17941510.156125902741100
3.55-3.830.15851400.139126012741100
3.83-4.210.14571420.124225942736100
4.21-4.820.14131390.119226212760100
4.82-6.070.17891480.144426402788100
6.07-47.180.1871180.152628222940100

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