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- PDB-2pey: Crystal structure of deletion mutant of APS-kinase domain of huma... -

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Basic information

Entry
Database: PDB / ID: 2pey
TitleCrystal structure of deletion mutant of APS-kinase domain of human PAPS-synthetase 1
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)
KeywordsTRANSFERASE / protein-nucleic acid complex / NMP-kinase fold
Function / homology
Function and homology information


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 / nucleotidyltransferase activity / skeletal system development ...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 / nucleotidyltransferase activity / skeletal system development / Signaling by BRAF and RAF1 fusions / phosphorylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate 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 / Adenylylsulphate kinase / Adenylyl-sulfate 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'-PHOSPHOSULFATE / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSekulic, N. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural mechanism for substrate inhibition of the adenosine 5'-phosphosulfate kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 and its ramifications for enzyme regulation.
Authors: Sekulic, N. / Konrad, M. / Lavie, A.
History
DepositionApr 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_ref_seq_dif.details ..._struct.title / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9995
Polymers39,7492
Non-polymers1,2503
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.430, 59.750, 138.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)


Mass: 19874.469 Da / Num. of mol.: 2 / Fragment: APS-kinase domain (residues 51-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1, ATPSK1, PAPSS
Plasmid: pGEX-RB in which the thrombin site was replaced by TEV cutting site
Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 codon plus / References: UniProt: O43252, adenylyl-sulfate kinase
#2: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE / 3'-Phosphoadenosine-5'-phosphosulfate


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Chemical ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP / Deoxyadenosine diphosphate


Mass: 411.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O9P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: reservoir: 16-20% PEG 3350, 0.25-0.15 M diammonium hydrogen citrate, drop: 3.2 mg/ml protein solution, 2mM dADP, 2mM APS, 5mM MgCl2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. all: 30062 / Num. obs: 29201 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 8.4 / Net I/σ(I): 16.63
Reflection shellResolution: 1.88→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.14 / Num. unique all: 3922 / Rsym value: 38.7 / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OFX

2ofx


Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.634 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25344 2915 10.1 %RANDOM
Rwork0.19869 ---
obs0.20414 26048 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.686 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2---0.78 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 79 172 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222706
X-RAY DIFFRACTIONr_angle_refined_deg1.4872.0023684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91724.884129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31815443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6741518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022046
X-RAY DIFFRACTIONr_nbd_refined0.2010.21187
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.210
X-RAY DIFFRACTIONr_mcbond_it0.8541.51691
X-RAY DIFFRACTIONr_mcangle_it1.41822658
X-RAY DIFFRACTIONr_scbond_it2.15731147
X-RAY DIFFRACTIONr_scangle_it3.3274.51026
LS refinement shellResolution: 1.88→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 159 -
Rwork0.332 1325 -
obs--69.15 %

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