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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) / : / : / regulation of protein localization => GO:0032880 / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER ...: / : / regulation of single strand break repair / HDR through MMEJ (alt-NHEJ) / : / : / regulation of protein localization => GO:0032880 / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / : / SUMOylation of DNA damage response and repair proteins / pentosyltransferase activity / cellular response to superoxide / : / POLB-Dependent Long Patch Base Excision Repair / regulation of growth rate / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of myofibroblast differentiation / : / negative regulation of ATP biosynthetic process / positive regulation of single strand break repair / NAD DNA ADP-ribosyltransferase activity / voluntary musculoskeletal movement / DNA ADP-ribosylation / mitochondrial DNA metabolic process / 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 / regulation of catalytic activity / positive regulation of transcription regulatory region DNA binding / : / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / positive regulation of intracellular estrogen receptor signaling pathway / protein auto-ADP-ribosylation / DNA metabolic process / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / positive regulation of double-strand break repair via homologous recombination / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / SMAD binding / behavioral response to cocaine / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / R-SMAD binding / positive regulation of SMAD protein signal transduction / transcription factor binding / protein autoprocessing / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / cellular response to transforming growth factor beta stimulus / telomere maintenance / mitochondrion organization / transforming growth factor beta receptor signaling pathway / nuclear estrogen receptor binding / protein-DNA complex / response to gamma radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / base-excision repair / protein modification process / positive regulation of protein localization to nucleus / histone deacetylase binding / cellular response to insulin stimulus / cellular response to amyloid-beta / cellular response to UV / NAD binding / double-strand break repair / site of double-strand break / nuclear envelope / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / nuclear body / apoptotic process / DNA damage response / chromatin binding / nucleolus / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / 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 / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / 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 / 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

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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


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
Non-polymers00
Water0
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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