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- PDB-4fvt: Human SIRT3 bound to Ac-ACS peptide and Carba-NAD -

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Basic information

Entry
Database: PDB / ID: 4fvt
TitleHuman SIRT3 bound to Ac-ACS peptide and Carba-NAD
Components
  • Acetylated ACS2 peptide
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Sirtuin / Carba-NAD
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / mitochondrial matrix / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.47 Å
AuthorsDai, H.
CitationJournal: J.Org.Chem. / Year: 2012
Title: Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5.
Authors: Szczepankiewicz, B.G. / Dai, H. / Koppetsch, K.J. / Qian, D. / Jiang, F. / Mao, C. / Perni, R.B.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references

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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: Acetylated ACS2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2068
Polymers31,0982
Non-polymers1,1086
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.430, 131.050, 77.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 30553.260 Da / Num. of mol.: 1 / Fragment: UNP residues 122-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Acetylated ACS2 peptide


Mass: 544.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Ac-ACS2 peptide

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Non-polymers , 5 types, 61 molecules

#3: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.2M lithium sulfate monohydrate, 15% (w/v) poly-ethylene glycol (PEG) 12000, and 0.1 M Bis-Tris, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97849 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.47→38.72 Å / Num. all: 13699 / Num. obs: 13699 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 3.6
Reflection shellResolution: 2.47→2.53 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→38.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24889 727 5 %RANDOM
Rwork0.20207 ---
obs0.2044 13699 99.79 %-
all-13699 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.762 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.47→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 66 55 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3162.0223148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8823.02196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9691518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221733
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_it3.3541.51396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.78522268
X-RAY DIFFRACTIONr_scbond_it5.4113913
X-RAY DIFFRACTIONr_scangle_it7.0274.5880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 63 -
Rwork0.286 976 -
obs--100 %

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