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- PDB-9bpy: Human PARP1 ART domain bound to NAD+ analogs benzamide adenine di... -

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Basic information

Entry
Database: PDB / ID: 9bpy
TitleHuman PARP1 ART domain bound to NAD+ analogs benzamide adenine dinucleotide and carba-NAD+
ComponentsPoly [ADP-ribose] polymerase 1
KeywordsTRANSFERASE / PARP1 / NAD+ analog / ADP-ribosyl transferase
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / mitochondrial DNA metabolic process / regulation of circadian sleep/wake cycle, non-REM sleep ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / mitochondrial DNA metabolic process / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / non-sequence-specific DNA binding, bending / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / single-strand break-containing DNA binding / mitochondrial DNA repair / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / ATP generation from poly-ADP-D-ribose / replication fork reversal / positive regulation of necroptotic process / establishment of protein localization to chromatin / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of mitochondrial depolarization / HDR through MMEJ (alt-NHEJ) / single strand break repair / positive regulation of DNA-templated transcription, elongation / transcription regulator activator activity / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / cellular response to zinc ion / positive regulation of cardiac muscle hypertrophy / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of cGAS/STING signaling pathway / negative regulation of transcription elongation by RNA polymerase II / decidualization / NAD+-protein mono-ADP-ribosyltransferase activity / response to aldosterone / protein autoprocessing / macrophage differentiation / R-SMAD binding / nuclear replication fork / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of adipose tissue development / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / transforming growth factor beta receptor signaling pathway / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / protein localization to chromatin / nucleosome binding / response to gamma radiation / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / protein modification process / site of DNA damage / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / positive regulation of protein localization to nucleus / protein-DNA complex / fibrillar center / transcription by RNA polymerase II / NAD binding / DNA Damage Recognition in GG-NER / cellular response to amyloid-beta / histone deacetylase binding / enzyme activator activity / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / cellular response to UV / cellular response to insulin stimulus / regulation of protein localization / nuclear envelope / site of double-strand break / transcription regulator complex / cellular response to oxidative stress / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / nuclear body / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / chromosome / apoptotic process / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / DNA damage response / nucleolus / protein kinase binding
Similarity search - Function
Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-DQV / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLangelier, M.F. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT173370 Canada
CitationJournal: Mol.Cell / Year: 2024
Title: PARP enzyme de novo synthesis of protein-free poly(ADP-ribose).
Authors: Langelier, M.F. / Mirhasan, M. / Gilbert, K. / Sverzhinksy, A. / Furtos, A. / Pascal, J.M.
History
DepositionMay 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
C: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3259
Polymers120,0134
Non-polymers3,3125
Water18010
1
A: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3283
Polymers30,0031
Non-polymers1,3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6662
Polymers30,0031
Non-polymers6621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6662
Polymers30,0031
Non-polymers6621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6662
Polymers30,0031
Non-polymers6621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.664, 74.142, 85.182
Angle α, β, γ (deg.)98.49, 105.16, 104.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 30003.275 Da / Num. of mol.: 4 / Fragment: ADP-ribosyltransferase (ART) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-DQV / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 662.437 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: PARP1 ART (30 mg/ml) was crystallized in the presence of 1.6 mM BAD in 24 to 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.8→19.95 Å / Num. obs: 23920 / % possible obs: 97.9 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.044 / Rrim(I) all: 0.099 / Χ2: 0.95 / Net I/σ(I): 12.4
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 97.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.314 / Num. measured all: 16836 / Num. unique obs: 3494 / CC1/2: 0.608 / Rpim(I) all: 0.661 / Rrim(I) all: 1.475 / Χ2: 0.75 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 61.594 / SU ML: 0.494 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25758 1182 4.9 %RANDOM
Rwork0.22428 ---
obs0.22588 22735 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.99 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20.32 Å2-0.14 Å2
2--1.46 Å21.12 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 220 10 7652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127848
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167472
X-RAY DIFFRACTIONr_angle_refined_deg0.8821.67210647
X-RAY DIFFRACTIONr_angle_other_deg0.2971.58517293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.002537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.217101377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0390.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021678
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8754.3483757
X-RAY DIFFRACTIONr_mcbond_other1.8764.3483755
X-RAY DIFFRACTIONr_mcangle_it3.2467.8194675
X-RAY DIFFRACTIONr_mcangle_other3.2467.8194675
X-RAY DIFFRACTIONr_scbond_it1.5144.4134091
X-RAY DIFFRACTIONr_scbond_other1.5144.4134091
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6818.1035972
X-RAY DIFFRACTIONr_long_range_B_refined5.42440.488390
X-RAY DIFFRACTIONr_long_range_B_other5.42440.488391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 85 -
Rwork0.364 1618 -
obs--96.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8526-0.8375-0.75065.1375-1.10255.78350.10410.05510.4490.0395-0.1110.4447-0.46090.04610.00690.7683-0.0539-0.02210.33210.03040.0967-13.57732.12339.343
24.69431.181-1.06423.9088-0.73716.3109-0.04930.0016-0.4934-0.0090.1453-0.19140.1703-0.2134-0.0960.6389-0.03110.02840.36040.03980.1484-28.8152.15928.183
35.1369-2.2115-2.3363.67030.32755.8014-0.13040.6373-0.3229-0.17480.0742-0.28790.21850.01180.05630.8482-0.12550.04690.6855-0.05460.1023-9.6677.284-9.217
43.84010.4440.60654.1675-0.48765.7763-0.1450.01610.33720.34910.1142-0.0518-0.32980.15860.03080.8572-0.0825-0.13790.56970.18440.1041-17.97440.565-4.161
530.873320.252-41.352114.1631-16.5401188.6098-2.22472.0814-1.225-0.94941.2972-0.745812.241-5.24780.92752.4859-0.3998-0.58411.08020.30740.4184-3.82223.55842.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A765 - 1010
2X-RAY DIFFRACTION2B765 - 1010
3X-RAY DIFFRACTION3C767 - 1010
4X-RAY DIFFRACTION4D765 - 1011
5X-RAY DIFFRACTION5A1201 - 1203

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