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- PDB-2mzd: Characterization of the p300 Taz2-p53 TAD2 Complex and Comparison... -

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Basic information

Entry
Database: PDB / ID: 2mzd
TitleCharacterization of the p300 Taz2-p53 TAD2 Complex and Comparison with the p300 Taz2-p53 TAD1 Complex
Components
  • Cellular tumor antigen p53
  • Histone acetyltransferase p300
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity ...behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / cellular response to L-leucine / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / positive regulation by host of viral transcription / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of mitochondrion organization / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / positive regulation of programmed necrotic cell death / RUNX3 regulates NOTCH signaling / face morphogenesis / mRNA transcription / bone marrow development / circadian behavior / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / histone deacetylase regulator activity / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / NOTCH3 Intracellular Domain Regulates Transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / platelet formation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / megakaryocyte development / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / macrophage derived foam cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / nuclear androgen receptor binding / regulation of tubulin deacetylation / negative regulation of neuroblast proliferation / STAT family protein binding / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment
Similarity search - Function
CREB-binding Protein; Chain A / TAZ domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP ...CREB-binding Protein; Chain A / TAZ domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / Zinc finger ZZ-type signature. / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMiller Jenkins, L.M. / Feng, H. / Durell, S.R. / Tagad, H.D. / Mazur, S.J. / Tropea, J.E. / Bai, Y. / Appella, E.
CitationJournal: Biochemistry / Year: 2015
Title: Characterization of the p300 Taz2-p53 TAD2 Complex and Comparison with the p300 Taz2-p53 TAD1 Complex.
Authors: Miller Jenkins, L.M. / Feng, H. / Durell, S.R. / Tagad, H.D. / Mazur, S.J. / Tropea, J.E. / Bai, Y. / Appella, E.
History
DepositionFeb 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Histone acetyltransferase p300
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)12,8152
Polymers12,8152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-21 kcal/mol
Surface area6490 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 40000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300


Mass: 9963.786 Da / Num. of mol.: 1 / Fragment: UNP residues 1723-1812 / Mutation: C16A, C24A, C67A, C68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pJT57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09472, histone acetyltransferase
#2: Protein/peptide Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 2851.079 Da / Num. of mol.: 1 / Fragment: UNP residues 35-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-1H NOESY
1333D CBCA(CO)NH
1433D HN(CA)CB
1533D HNCO
1633D HN(CA)CO
1733D HNCA
1833D H(CCO)NH
1933D (H)CCH-TOCSY
11023D HNHA
11123D 1H-15N NOESY
11233D 1H-13C NOESY
11312D 1H-15N HSQC
11413D CBCA(CO)NH
11513D HN(CA)CB
11613D HNCA
11713D HNCO
11813D HN(CA)CO
11913D H(CCO)NH
12013D (H)CCH-TOCSY
12113D 1H-15N NOESY
12213D 1H-13C NOESY
12333D HBHA(CO)NH
12413D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM Taz2 domain of Histone Acetyltransferase p300, 1.0 mM [U-100% 13C; U-100% 15N] TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 15N] Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMTaz2 domain of Histone Acetyltransferase p300-11
1.0 mMTAD2 sub-domain of Cellular Tumor Antigen p53-2[U-100% 13C; U-100% 15N]1
1.0 mMTaz2 domain of Histone Acetyltransferase p300-3[U-100% 15N]2
1.1 mMTAD2 sub-domain of Cellular Tumor Antigen p53-42
1.0 mMTaz2 domain of Histone Acetyltransferase p300-5[U-100% 13C; U-100% 15N]3
1.1 mMTAD2 sub-domain of Cellular Tumor Antigen p53-63
1.0 mMTaz2 domain of Histone Acetyltransferase p300-74
1.1 mMTAD2 sub-domain of Cellular Tumor Antigen p53-84
Sample conditionsIonic strength: 200 / pH: 6.3 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40000 / Conformers submitted total number: 15

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