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- PDB-2pez: Crystal structrue of deletion mutant of APS-kinase domain of huma... -

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Basic information

Entry
Database: PDB / ID: 2pez
TitleCrystal structrue of deletion mutant of APS-kinase domain of human PAPS-synthetase 1 in complex with cyclic PAPS and dADP
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)
KeywordsTRANSFERASE / NMP-kinase fold / protein in complex with nucleic acid
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 / protein homodimerization activity / ATP binding / nucleus / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-DIPHOSPHATE / Chem-GGZ / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,0615
Polymers39,7492
Non-polymers1,3123
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.090, 59.400, 139.020
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 clevage site was replaced by TEV site
Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Codon plus / References: UniProt: O43252
#2: Chemical ChemComp-GGZ / (2S,3AR,4R,6R,6AR)-4-(6-AMINO-9H-PURIN-9-YL)-6-({[(R)-HYDROXY(SULFOOXY)PHOSPHORYL]OXY}METHYL)TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-2-OL 2-OXIDE


Mass: 489.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O12P2S
#3: Chemical ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


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


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
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, 2mM dADP, 2mM PAPS, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 73074 / Num. obs: 64712 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 5.1 / Net I/σ(I): 15.73
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.3 / Num. unique all: 11674 / Rsym value: 30.2 / % possible all: 87

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Processing

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

2pey


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.037 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21981 6493 10.1 %RANDOM
Rwork0.19433 ---
obs0.19695 57725 87.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.825 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 82 331 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222750
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.0073743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55424.884129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4931518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022061
X-RAY DIFFRACTIONr_nbd_refined0.2150.21344
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.221
X-RAY DIFFRACTIONr_mcbond_it1.1311.51711
X-RAY DIFFRACTIONr_mcangle_it1.6522695
X-RAY DIFFRACTIONr_scbond_it2.64431149
X-RAY DIFFRACTIONr_scangle_it3.9654.51048
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 427 -
Rwork0.255 3935 -
obs--81.95 %

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