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- PDB-2le0: PARP BRCT Domain -

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Basic information

Entry
Database: PDB / ID: 2le0
TitlePARP BRCT Domain
ComponentsPoly [ADP-ribose] polymerase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of single strand break repair / HDR through MMEJ (alt-NHEJ) / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / DNA Damage Recognition in GG-NER / pentosyltransferase activity / SUMOylation of DNA damage response and repair proteins / cellular response to superoxide / transcription pausing by RNA polymerase II / POLB-Dependent Long Patch Base Excision Repair ...regulation of single strand break repair / HDR through MMEJ (alt-NHEJ) / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / DNA Damage Recognition in GG-NER / pentosyltransferase activity / SUMOylation of DNA damage response and repair proteins / cellular response to superoxide / transcription pausing by RNA polymerase II / POLB-Dependent Long Patch Base Excision Repair / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of growth rate / 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 / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / negative regulation of adipose tissue development / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / ATP generation from poly-ADP-D-ribose / replication fork reversal / positive regulation of necroptotic process / signal transduction involved in regulation of gene expression / transcription regulator activator activity / response to aldosterone / negative regulation of interleukin-17 production / protein localization to site of double-strand break / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / positive regulation of intracellular estrogen receptor signaling pathway / protein poly-ADP-ribosylation / DNA metabolic process / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / positive regulation of mitochondrial depolarization / protein autoprocessing / cellular response to zinc ion / decidualization / nuclear replication fork / R-SMAD binding / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of SMAD protein signal transduction / negative regulation of transcription elongation by RNA polymerase II / NAD+ poly-ADP-ribosyltransferase activity / cellular response to transforming growth factor beta stimulus / nucleosome binding / positive regulation of double-strand break repair via homologous recombination / site of DNA damage / behavioral response to cocaine / protein localization to chromatin / nucleotidyltransferase activity / positive regulation of adipose tissue development / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / cellular response to nerve growth factor stimulus / protein-DNA complex / base-excision repair / positive regulation of protein localization to nucleus / double-strand break repair via homologous recombination / enzyme activator activity / cellular response to amyloid-beta / NAD binding / histone deacetylase binding / cellular response to insulin stimulus / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process
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 / BRCT domain / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. ...Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / BRCT domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailslowest energy, model 1
AuthorsMueller, G. / Loeffler, P. / Cuneo, M. / Derose, E. / London, R.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Structural studies of the PARP-1 BRCT domain.
Authors: Loeffler, P.A. / Cuneo, M.J. / Mueller, G.A. / Derose, E.F. / Gabel, S.A. / London, R.E.
History
DepositionJun 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)11,6731
Polymers11,6731
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11672.600 Da / Num. of mol.: 1 / Fragment: BRCT domain residues 389-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Parp1, Adprt / Production host: Escherichia coli (E. coli) / References: UniProt: P27008, NAD+ ADP-ribosyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D C(CO)NH
1613D H(CCO)NH
171(HB)CB(CGCD)HD
181(HB)CB(CGCDCE)HE
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 3 mM [U-100% 13C; U-100% 15N] protein, 40 mM sodium phosphate, 140 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMprotein-1[U-100% 13C; U-100% 15N]1
40 mMsodium phosphate-21
140 mMsodium chloride-31
Sample conditionsIonic strength: 0.18 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
VnmrJVariancollection
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANASchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
Details: Final Refinement from cyana generated restraints, Multiple rounds of calculations
NMR constraintsNOE constraints total: 1631 / NOE intraresidue total count: 449 / NOE long range total count: 412 / NOE medium range total count: 323 / NOE sequential total count: 447
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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