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- PDB-2cr9: Solution structure of WGR domain of poly(ADP-ribose) polymerase-1 -

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Entry
Database: PDB / ID: 2cr9
TitleSolution structure of WGR domain of poly(ADP-ribose) polymerase-1
ComponentsPoly [ADP-ribose] polymerase-1
KeywordsTRANSFERASE / parp / DNA repair / necrosis / apoptosis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process ...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 / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / 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 / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / single strand break repair / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / cellular response to zinc ion / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / decidualization / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / protein autoprocessing / macrophage differentiation / R-SMAD binding / nuclear replication fork / negative regulation of adipose tissue development / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / 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 / cellular response to nerve growth factor stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of protein localization to nucleus / protein-DNA complex / fibrillar center / transcription by RNA polymerase II / DNA Damage Recognition in GG-NER / NAD binding / cellular response to amyloid-beta / enzyme activator activity / histone deacetylase binding / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / cellular response to UV / double-strand break repair / cellular response to insulin stimulus / nuclear envelope / regulation of protein localization / site of double-strand break / transcription regulator complex / cellular response to oxidative stress / damaged DNA binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / apoptotic process / chromatin binding / DNA damage response / nucleolus
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
Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of WGR domain of poly(ADP-ribose) polymerase-1
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase-1


Theoretical massNumber of molelcules
Total (without water)15,4421
Polymers15,4421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Poly [ADP-ribose] polymerase-1 / PARP-1 / ADPRT / NAD+ / ADP-ribosyltransferase-1 / Poly[ADP-ribose] synthetase-1


Mass: 15442.455 Da / Num. of mol.: 1 / Fragment: WGR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PARP1, ADPRT, PPOL / Plasmid: P040517-11 / References: UniProt: P09874, NAD+ ADP-ribosyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.15mM WGR domain U-13C,15N; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.structure solution
CYANA1.0.7Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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