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- PDB-4bhw: Structural basis for autoinhibition of the acetyltransferase acti... -

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Basic information

Entry
Database: PDB / ID: 4bhw
TitleStructural basis for autoinhibition of the acetyltransferase activity of p300
ComponentsHISTONE ACETYLTRANSFERASE P300
KeywordsTRANSFERASE / BROMODOMAIN / PHD DOMAIN / RING DOMAIN / HAT DOMAIN / ENHANCEOSOME
Function / homology
Function and homology information


behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation ...behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation / histone H2B acetyltransferase activity / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / thigmotaxis / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / positive regulation of TORC2 signaling / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / PI5P Regulates TP53 Acetylation / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / fat cell differentiation / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / histone acetyltransferase complex / canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NF-kappaB binding / negative regulation of gluconeogenesis / cellular response to nutrient levels / somitogenesis / negative regulation of protein-containing complex assembly / pre-mRNA intronic binding / Attenuation phase / positive regulation of T-helper 17 cell lineage commitment / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / skeletal muscle tissue development / regulation of cellular response to heat
Similarity search - Function
CREB-binding protein/p300 RING domain / Cysteine Rich Protein / 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/p300 RING domain / Cysteine Rich Protein / 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 / : / Histone acetyltransferase p300-like, PHD domain / 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 / Zinc finger ZZ-type signature. / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Ribbon / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-01K / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.799 Å
AuthorsDelvecchio, M. / Gaucher, J. / Aguilar-Gurrieri, C. / Ortega, E. / Panne, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of the P300 Catalytic Core and Implications for Chromatin Targeting and Hat Regulation
Authors: Delvecchio, M. / Gaucher, J. / Aguilar-Gurrieri, C. / Ortega, E. / Panne, D.
History
DepositionApr 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Database references
Revision 2.0Apr 3, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _atom_site.occupancy / _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE ACETYLTRANSFERASE P300
B: HISTONE ACETYLTRANSFERASE P300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,65311
Polymers134,2052
Non-polymers2,4479
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-116.4 kcal/mol
Surface area57350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.051, 92.894, 123.309
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2043-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9561, -0.0444, 0.2895), (-0.043, -0.999, -0.0112), (0.2897, -0.0018, -0.9571)
Vector: -11.5577, -36.5049, 72.0321)

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Components

#1: Protein HISTONE ACETYLTRANSFERASE P300 / P300 HAT / E1A-ASSOCIATED PROTEIN P300


Mass: 67102.695 Da / Num. of mol.: 2 / Fragment: P300 CORE, RESIDUES 1043-1519,1581-1666 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-01K / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate / Lysine-COENZYME A derivative


Mass: 994.794 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H53N10O19P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES, PH 7.5, 20% PEG3350, 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.282
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 80344 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3BIY

3biy


Resolution: 2.799→46.62 Å / SU ML: 0.37 / σ(F): 1.2 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 4056 5.1 %
Rwork0.2077 --
obs0.2096 80344 97.05 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.313 Å2 / ksol: 0.274 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.097 Å20 Å21.3803 Å2
2--8.8622 Å2-0 Å2
3----6.7652 Å2
Refinement stepCycle: LAST / Resolution: 2.799→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 135 82 9394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069595
X-RAY DIFFRACTIONf_angle_d1.10213011
X-RAY DIFFRACTIONf_dihedral_angle_d14.5473626
X-RAY DIFFRACTIONf_chiral_restr0.2331349
X-RAY DIFFRACTIONf_plane_restr0.0031678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7989-2.83180.3422980.34182063X-RAY DIFFRACTION77
2.8318-2.86630.37341380.34512635X-RAY DIFFRACTION97
2.8663-2.90260.37131380.29482570X-RAY DIFFRACTION94
2.9026-2.94080.2641170.29592598X-RAY DIFFRACTION98
2.9408-2.9810.3721440.28752677X-RAY DIFFRACTION95
2.981-3.02360.32511560.2852535X-RAY DIFFRACTION96
3.0236-3.06880.3581320.28162582X-RAY DIFFRACTION96
3.0688-3.11670.29431180.26822603X-RAY DIFFRACTION95
3.1167-3.16780.31731630.26832612X-RAY DIFFRACTION97
3.1678-3.22240.26651340.25592589X-RAY DIFFRACTION95
3.2224-3.2810.26741360.2652599X-RAY DIFFRACTION97
3.281-3.34410.31531470.26622602X-RAY DIFFRACTION96
3.3441-3.41230.30981610.24242615X-RAY DIFFRACTION98
3.4123-3.48650.32141320.25842588X-RAY DIFFRACTION96
3.4865-3.56750.25991570.23272656X-RAY DIFFRACTION97
3.5675-3.65670.27121280.22582676X-RAY DIFFRACTION98
3.6567-3.75560.24881300.21612675X-RAY DIFFRACTION97
3.7556-3.8660.21741320.19792725X-RAY DIFFRACTION99
3.866-3.99070.21291500.19552607X-RAY DIFFRACTION99
3.9907-4.13330.24251690.17772696X-RAY DIFFRACTION100
4.1333-4.29870.18491440.16992709X-RAY DIFFRACTION100
4.2987-4.49420.23051420.14882726X-RAY DIFFRACTION100
4.4942-4.73090.17311280.16052711X-RAY DIFFRACTION100
4.7309-5.0270.19061370.17472684X-RAY DIFFRACTION100
5.027-5.41460.25291330.2022708X-RAY DIFFRACTION100
5.4146-5.95850.23691410.20432780X-RAY DIFFRACTION100
5.9585-6.81840.27121750.20952651X-RAY DIFFRACTION100
6.8184-8.58170.18681320.1652707X-RAY DIFFRACTION100
8.5817-46.62620.18311440.16432709X-RAY DIFFRACTION99
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)
10.5198-0.31990.08650.157-0.0280.4836-0.0530.11130.146-0.3445-0.19290.0241-0.2472-0.6902-0.32320.83460.433-0.07150.98010.09240.5263-48.43615.90325.5646
20.38290.0590.0107-0.045-0.16950.2091-0.07410.4210.0420.0001-0.33010.48950.5507-0.2928-0.06590.8275-0.03490.20010.423-0.02460.6089-59.2603-11.664554.3268
30.28270.3559-0.36691.4117-0.66231.19070.08280.00490.0416-0.0534-0.11610.01420.0784-0.0828-0.06760.0838-0.0005-0.03510.21850.00840.283-27.9293-19.640856.9861
40.30930.11740.4380.37570.21230.85890.2988-0.06840.24340.0422-0.36420.02840.0273-0.83770.03160.13370.16630.0410.3670.05620.5324-34.573-3.638354.6135
50.26890.1296-0.09930.1263-0.21180.2524-0.05820.1854-0.11960.0096-0.11920.13270.505-0.676-0.00021.0021-0.31970.08650.9396-0.0120.5819-50.7295-40.745133.3945
60.0865-0.05780.0876-0.1115-0.0801-0.01240.0811-0.07330.1621-0.1325-0.37790.4224-0.2653-0.1807-0.00011.17870.1276-0.15430.7152-0.06680.72-53.6166-23.86942.6811
7-0.09-0.0034-0.10611.2243-0.22741.33910.00890.011-0.0214-0.1921-0.1387-0.15250.13630.1011-0.00160.44010.10370.06670.34720.05910.3209-20.9561-17.977910.6488
80.24620.1040.090.5034-0.31520.33690.12670.11240.0203-0.2481-0.1631-0.05940.1301-0.111200.70650.06740.07980.4587-0.01240.4052-23.511-17.82015.8442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1046:1179)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1180:1243)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1244:1621)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 1622:1664)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 1046:1179)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1180:1243)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 1244:1520)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 1521:1664)

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