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- PDB-8h6c: Crystal structure of human GCN5 histone acetyltransferase domain ... -

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Basic information

Entry
Database: PDB / ID: 8h6c
TitleCrystal structure of human GCN5 histone acetyltransferase domain bound with malonyl-CoA
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication / regulation of regulatory T cell differentiation / transcription factor TFTC complex / telencephalon development / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Cardiogenesis / limb development / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / regulation of T cell activation / NOTCH3 Intracellular Domain Regulates Transcription / protein-lysine-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / midbrain development / Formation of paraxial mesoderm / histone acetyltransferase activity / intracellular distribution of mitochondria / regulation of RNA splicing / regulation of cell division / regulation of embryonic development / RNA Polymerase I Transcription Initiation / histone acetyltransferase complex / long-term memory / negative regulation of gluconeogenesis / somitogenesis / regulation of DNA repair / 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 / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of gluconeogenesis / positive regulation of cytokine production / gluconeogenesis / neural tube closure / cellular response to nerve growth factor stimulus / response to nutrient levels / : / regulation of protein stability / multicellular organism growth / regulation of synaptic plasticity / B-WICH complex positively regulates rRNA expression / Pre-NOTCH Transcription and Translation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / mitotic spindle / cellular response to tumor necrosis factor / HATs acetylate histones / heart development / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
MALONYL-COENZYME A / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, N. / Tao, Y.J. / Guo, Y.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch Foundation United States
CitationJournal: Res / Year: 2023
Title: Molecular Basis of KAT2A Selecting Acyl-CoA Cofactors for Histone Modifications.
Authors: Li, S. / Li, N. / He, J. / Zhou, R. / Lu, Z. / Tao, Y.J. / Guo, Y.R. / Wang, Y.
History
DepositionOct 16, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Histone acetyltransferase KAT2A
D: Histone acetyltransferase KAT2A
E: Histone acetyltransferase KAT2A
F: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
A: Histone acetyltransferase KAT2A
G: Histone acetyltransferase KAT2A
H: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,92916
Polymers154,1008
Non-polymers6,8298
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.692, 175.692, 175.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Histone acetyltransferase KAT2A / General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hGCN5 / ...General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hGCN5 / Histone glutaryltransferase KAT2A / Histone succinyltransferase KAT2A / Lysine acetyltransferase 2A / STAF97


Mass: 19262.529 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q92830, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H38N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.6M Ammonium sulfate, 0.1M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 62374 / % possible obs: 100 % / Redundancy: 18.8 % / Biso Wilson estimate: 49.51 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.029 / Rrim(I) all: 0.127 / Χ2: 1.362 / Net I/σ(I): 5.9 / Num. measured all: 1174826
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.5-2.5418.80.78230740.9180.1850.8030.724
2.54-2.5919.10.71330810.9410.1670.7320.739
2.59-2.6419.10.61430880.9560.1440.630.769
2.64-2.6919.10.54531020.9620.1280.5590.782
2.69-2.7519.10.49730500.9680.1170.5110.816
2.75-2.8219.10.4231340.9730.0980.4310.838
2.82-2.8919.10.34931080.9820.0820.3580.894
2.89-2.9619.10.2930710.9860.0680.2980.961
2.96-3.05190.25130810.9890.0590.2581.033
3.05-3.15190.21931240.9910.0510.2251.127
3.15-3.26190.18731110.9920.0440.1921.294
3.26-3.3918.90.15930930.9940.0370.1631.533
3.39-3.5518.90.13731280.9950.0320.1411.656
3.55-3.7318.90.11731100.9960.0280.1211.669
3.73-3.9718.90.10231150.9970.0240.1051.805
3.97-4.2718.70.09631370.9970.0230.0992.023
4.27-4.718.50.09231500.9970.0220.0942.333
4.7-5.3818.40.0931450.9980.0220.0932.359
5.38-6.7818.60.08331780.9980.020.0851.726
6.78-5017.30.07132940.9990.0170.0742.223

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRM

5trm


Resolution: 2.5→43.92 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 3168 5.13 %
Rwork0.1919 58599 -
obs0.1942 61767 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.28 Å2 / Biso mean: 49.9128 Å2 / Biso min: 27.4 Å2
Refinement stepCycle: final / Resolution: 2.5→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10655 0 426 232 11313
Biso mean--57.26 47.67 -
Num. residues----1300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.34321310.24332482261398
2.54-2.580.29741490.22572517266698
2.58-2.620.29791650.22442463262898
2.62-2.670.27781300.222504263498
2.67-2.720.28631240.22382491261598
2.72-2.770.31971450.23192525267099
2.77-2.820.28531120.22422542265499
2.82-2.880.28991590.22172518267799
2.89-2.950.28431530.22812500265399
2.95-3.030.29531320.21822555268799
3.03-3.110.28341520.23162504265699
3.11-3.20.26071450.21212555270099
3.2-3.30.27991540.197525352689100
3.3-3.420.27331110.193925792690100
3.42-3.560.23531710.186125362707100
3.56-3.720.21391440.187525512695100
3.72-3.910.19431040.165926132717100
3.92-4.160.17891170.157925852702100
4.16-4.480.17781400.161126092749100
4.48-4.930.18041080.147125872695100
4.93-5.640.23591490.182726152764100
5.65-7.10.2971030.231626492752100
7.11-43.920.20771700.19442584275496

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