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- PDB-5bwn: Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myris... -

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Basic information

Entry
Database: PDB / ID: 5bwn
TitleCrystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • myristoyl H3K9 peptide
KeywordsPEPTIDE/HYDROLASE / Hydrolase / PEPTIDE-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / nucleosomal DNA binding / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / euchromatin / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / structural constituent of chromatin / nucleosome / positive regulation of cell growth / sequence-specific DNA binding / mitochondrial matrix / protein heterodimerization activity / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.3C / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.942 Å
AuthorsGai, W. / Liu, D.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structures of SIRT3 reveal that the alpha 2-alpha 3 loop and alpha 3-helix affect the interaction with long-chain acyl lysine.
Authors: Gai, W. / Li, H. / Jiang, H. / Long, Y. / Liu, D.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: myristoyl H3K9 peptide
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7703
Polymers35,7052
Non-polymers651
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.102, 54.691, 117.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide myristoyl H3K9 peptide


Mass: 1302.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q6NXT2*PLUS
#2: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 34402.445 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 118-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium tartrate dibasic (pH 7.0), 20% w/v PEG 3350, 0.01M Urea

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 21698 / % possible obs: 96 % / Redundancy: 11.98 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.2
Reflection shellResolution: 1.94→1.99 Å / Mean I/σ(I) obs: 5.2 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHENIX1.10.1-2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLT

3glt


Resolution: 1.942→41.279 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 1998 9.61 %RANDOM
Rwork0.2261 ---
obs0.2308 20783 96.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.942→41.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 1 111 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072282
X-RAY DIFFRACTIONf_angle_d0.9553102
X-RAY DIFFRACTIONf_dihedral_angle_d9.9211849
X-RAY DIFFRACTIONf_chiral_restr0.057349
X-RAY DIFFRACTIONf_plane_restr0.007402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9425-1.9910.34981440.28081347X-RAY DIFFRACTION98
1.991-2.04490.3231370.27431305X-RAY DIFFRACTION96
2.0449-2.1050.31181450.2481351X-RAY DIFFRACTION97
2.105-2.1730.31291390.23871314X-RAY DIFFRACTION97
2.173-2.25060.28631390.23251318X-RAY DIFFRACTION96
2.2506-2.34070.28521410.23561319X-RAY DIFFRACTION95
2.3407-2.44730.28081420.23091326X-RAY DIFFRACTION96
2.4473-2.57630.29091400.22861322X-RAY DIFFRACTION96
2.5763-2.73770.26161430.23291347X-RAY DIFFRACTION96
2.7377-2.9490.30021440.22361351X-RAY DIFFRACTION97
2.949-3.24560.27221450.2261370X-RAY DIFFRACTION98
3.2456-3.7150.27691480.21311377X-RAY DIFFRACTION97
3.715-4.67950.21781400.20291315X-RAY DIFFRACTION92
4.6795-41.28820.28231510.23061423X-RAY DIFFRACTION93

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