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- PDB-8i1n: Crystal structure of APSK2 domain from human PAPSS2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8i1n
TitleCrystal structure of APSK2 domain from human PAPSS2 in complex with endogenous APS and ADP
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
KeywordsBIOSYNTHETIC PROTEIN / Adenosine 5'-phosphosulfate kinase domain 2 / APSK2 / human PAPSS2
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 nucleotide triphosphate hydrolases ...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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-PHOSPHOSULFATE / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, L. / Song, W.Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2023
Title: Redox switching mechanism of the adenosine 5'-phosphosulfate kinase domain (APSK2) of human PAPS synthase 2.
Authors: Zhang, L. / Song, W. / Li, T. / Mu, Y. / Zhang, P. / Hu, J. / Lin, H. / Zhang, J. / Gao, H. / Zhang, L.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,80210
Polymers87,2394
Non-polymers2,5636
Water00
1
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)44,9015
Polymers43,6192
Non-polymers1,2823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-32 kcal/mol
Surface area16760 Å2
MethodPISA
2
C: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
D: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9015
Polymers43,6192
Non-polymers1,2823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-36 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.594, 71.329, 89.986
Angle α, β, γ (deg.)90.00, 114.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21809.680 Da / Num. of mol.: 4 / Fragment: APSK2 homodimer domain
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
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: 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
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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate dihydrate, pH7.0 and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21315 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.974 / Χ2: 0.097 / Net I/σ(I): 3.8 / Num. measured all: 132290
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.8-2.94.80.85420141.045196.1
2.9-3.025.60.79621291.076198.6
3.02-3.1560.63320961.089199.2
3.15-3.326.20.55321131.081198.9
3.32-3.536.20.37121141.1199.2
3.53-3.86.40.27521661.067199.2
3.8-4.186.90.19621451.061199.5
4.18-4.796.50.14421481.06199.6
4.79-6.036.70.13421830.983199.7
6.03-506.50.09822072.035199.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.2refinement
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFX

2ofx


Resolution: 2.8→44.19 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 1003 4.93 %
Rwork0.208 --
obs0.2116 20342 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6101 0 162 0 6263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116393
X-RAY DIFFRACTIONf_angle_d1.48671
X-RAY DIFFRACTIONf_dihedral_angle_d28.811967
X-RAY DIFFRACTIONf_chiral_restr0.084951
X-RAY DIFFRACTIONf_plane_restr0.0081117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.2803990.2452008X-RAY DIFFRACTION70
2.95-3.130.30941490.25632739X-RAY DIFFRACTION95
3.13-3.380.35621580.24572887X-RAY DIFFRACTION98
3.38-3.710.33961560.22742863X-RAY DIFFRACTION99
3.72-4.250.27361670.19392900X-RAY DIFFRACTION99
4.25-5.360.23631270.18162925X-RAY DIFFRACTION100
5.36-44.190.25011470.1893017X-RAY DIFFRACTION99

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