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- PDB-8v2n: Human SIRT3 co-crystallized with ligands, including p53-AMC pepti... -

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Basic information

Entry
Database: PDB / ID: 8v2n
TitleHuman SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD
Components
  • GLN-PRO-LYS-FDL
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Activator / Complex / Deacylase
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 / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 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 / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / 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 / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / 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
Similarity search - Domain/homology
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsChakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. ...Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: biorxiv / Year: 2023
Title: Computationally Driven Discovery and Characterization of SIRT3 Activating Compounds that Fully Recover Catalytic Activity under NAD+ Depletion
Authors: Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T.
History
DepositionNov 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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: GLN-PRO-LYS-FDL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7684
Polymers32,0402
Non-polymers7282
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.339, 53.178, 68.539
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial


Mass: 31340.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NTG7
#2: Protein/peptide GLN-PRO-LYS-FDL


Mass: 699.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.13 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M ...Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.74→42.04 Å / Num. obs: 25473 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.993 / Net I/σ(I): 7.4
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 1288 / CC1/2: 0.649

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→42.04 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.224 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28155 1259 4.9 %RANDOM
Rwork0.24186 ---
obs0.24383 24207 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.339 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20.19 Å2
2---0.56 Å20 Å2
3---1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.74→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 45 60 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8061.6653013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8725266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41220.561107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37515337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9882.4711065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8363.6951327
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5462.7671137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.67535.7393483
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.78 Å
RfactorNum. reflection% reflection
Rfree0.271 107 -
Rwork0.305 1779 -
obs--99.74 %

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