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- PDB-7r3l: PARP14 catalytic domain in complex with OUL40 -

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Basic information

Entry
Database: PDB / ID: 7r3l
TitlePARP14 catalytic domain in complex with OUL40
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE / Mono-ADP-transferase / Inhibitor / Complex
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme ...PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
6-methyl-[1,2,4]triazolo[3,4-b][1,3]benzothiazole / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaksimainen, M.M. / Murthy, S. / Lehtio, L.
Funding support Finland, 3items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
Academy of Finland287063 Finland
Academy of Finland294085 Finland
CitationJournal: J.Med.Chem. / Year: 2023
Title: [1,2,4]Triazolo[3,4- b ]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes.
Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite- ...Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite-Hyyrylainen, R. / Dreassi, E. / Luscher, B. / Korn, P. / Tabarrini, O. / Lehtio, L.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: 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

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 14
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8817
Polymers44,2372
Non-polymers6445
Water2,540141
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3433
Polymers22,1191
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5384
Polymers22,1191
Non-polymers4193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.884, 83.748, 80.028
Angle α, β, γ (deg.)90.000, 115.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1902-

CL

21B-1902-

CL

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Components

#1: Protein Poly [ADP-ribose] polymerase 14 / PARP-14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2


Mass: 22118.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Production host: Escherichia coli (E. coli) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-I1Q / 6-methyl-[1,2,4]triazolo[3,4-b][1,3]benzothiazole / 7-Methyl(1,2,4)triazolo(3,4-b)(1,3)benzothiazole


Mass: 189.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: . 0.17 M ammonium sulphate, 15% (v/v) glycerol, 27% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.999→53.1 Å / Num. obs: 32725 / % possible obs: 99.2 % / Redundancy: 3.1 % / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 1.999→2.033 Å / Num. unique obs: 1587 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GOY

3goy


Resolution: 2→53.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.019 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1583 4.8 %RANDOM
Rwork0.2025 ---
obs0.2041 31142 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.9 Å2 / Biso mean: 23.308 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å2-1.27 Å2
2--1.72 Å20 Å2
3----1.7 Å2
Refinement stepCycle: final / Resolution: 2→53.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 41 145 2856
Biso mean--39.73 26.16 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152495
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6623795
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5885725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55922.857168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5321515
X-RAY DIFFRACTIONr_chiral_restr0.0650.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.283 88 -
Rwork0.253 2302 -
obs--99.17 %

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