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- PDB-8hlw: Crystal structure of SIRT3 in complex with H4K16la peptide -

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Basic information

Entry
Database: PDB / ID: 8hlw
TitleCrystal structure of SIRT3 in complex with H4K16la peptide
Components
  • Histone H4 residues 20-27
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / SIRT3 / Lysine lactylation eraser
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / aerobic respiration / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Transcriptional activation of mitochondrial biogenesis / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of ERK1 and ERK2 cascade / DNA Damage/Telomere Stress Induced Senescence / positive regulation of insulin secretion / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / transferase activity / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromosome, telomeric region / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / enzyme binding / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / Histone H4 / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhuming, F. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Iscience / Year: 2023
Title: Identification of SIRT3 as an eraser of H4K16la.
Authors: Fan, Z. / Liu, Z. / Zhang, N. / Wei, W. / Cheng, K. / Sun, H. / Hao, Q.
History
DepositionDec 1, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: Histone H4 residues 20-27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3234
Polymers32,1672
Non-polymers1552
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.449, 97.449, 53.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 31253.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 162th-172th lost of electron density / Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase
#2: Protein/peptide Histone H4 residues 20-27


Mass: 914.091 Da / Num. of mol.: 1 / Fragment: residues 20-27, with lactylated No.23 lysine / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97847 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97847 Å / Relative weight: 1
ReflectionResolution: 2.5→45.24 Å / Num. obs: 19276 / % possible obs: 99.79 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.42 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.03693 / Rrim(I) all: 0.05222 / Net I/σ(I): 28.75
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.1884 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 1630 / CC1/2: 0.843 / CC star: 0.956 / Rpim(I) all: 0.1884 / Rrim(I) all: 0.2665 / % possible all: 98.61

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.24 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1004 9.89 %RANDOM
Rwork0.1878 ---
obs0.1932 10153 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 6 107 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032228
X-RAY DIFFRACTIONf_angle_d0.5973030
X-RAY DIFFRACTIONf_dihedral_angle_d4.79303
X-RAY DIFFRACTIONf_chiral_restr0.04341
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.30361420.23561280X-RAY DIFFRACTION99
2.63-2.80.30261440.22321291X-RAY DIFFRACTION100
2.8-3.010.32981440.2411295X-RAY DIFFRACTION100
3.01-3.320.2971460.20271298X-RAY DIFFRACTION100
3.32-3.80.23651400.18161311X-RAY DIFFRACTION100
3.8-4.780.19011450.15191318X-RAY DIFFRACTION100
4.78-45.240.20121430.17281356X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.6168 Å / Origin y: -12.1603 Å / Origin z: -1.2486 Å
111213212223313233
T0.2935 Å2-0.0299 Å2-0.0052 Å2-0.1682 Å2-0.0812 Å2--0.3275 Å2
L1.8023 °21.2889 °22.2614 °2-3.7277 °23.5926 °2--5.4798 °2
S-0.2788 Å °-0.0526 Å °0.1757 Å °-0.0409 Å °-0.068 Å °0.5409 Å °-0.0199 Å °-0.016 Å °0.0965 Å °
Refinement TLS groupSelection details: all

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