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- PDB-3glu: Crystal Structure of Human SIRT3 with AceCS2 peptide -

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Basic information

Entry
Database: PDB / ID: 3glu
TitleCrystal Structure of Human SIRT3 with AceCS2 peptide
Components
  • Acetyl-coenzyme A synthetase 2-like, mitochondrial
  • NAD-dependent deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE/HYDROLASE REGULATOR / NAD dependent deacetylase / sirtuin / product peptide complex / Hydrolase / Metal-binding / Mitochondrion / NAD / Polymorphism / Transit peptide / Zinc / Alternative splicing / Ligase / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity ...propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / ethanol catabolic process / Ethanol oxidation / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / acetyl-CoA biosynthetic process / 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 / AMP 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 / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / 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 / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / DHS-like NAD/FAD-binding domain superfamily / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / Acetyl-coenzyme A synthetase 2-like, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. ...Jin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. / Westphal, C.H. / Perni, R.B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of Human SIRT3 Displaying Substrate-induced Conformational Changes.
Authors: Jin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Choy, W. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. / Westphal, C.H. / Perni, R.B.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase sirtuin-3, mitochondrial
B: Acetyl-coenzyme A synthetase 2-like, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3485
Polymers33,0902
Non-polymers2583
Water1,22568
1
A: NAD-dependent deacetylase sirtuin-3, mitochondrial
B: Acetyl-coenzyme A synthetase 2-like, mitochondrial
hetero molecules

A: NAD-dependent deacetylase sirtuin-3, mitochondrial
B: Acetyl-coenzyme A synthetase 2-like, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,69510
Polymers66,1804
Non-polymers5156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3180 Å2
ΔGint-73 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.497, 129.460, 78.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31612.348 Da / Num. of mol.: 1 / Fragment: Human SIRT3, residues 118-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Plasmid: modified pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Acetyl-coenzyme A synthetase 2-like, mitochondrial / Acetate--CoA ligase 2 / Acetyl-CoA synthetase 2 / Acyl-CoA synthetase short-chain family member 1


Mass: 1477.846 Da / Num. of mol.: 1 / Fragment: Human Acyl-CoA, residues 638-649 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NUB1, acetate-CoA ligase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 68 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2008
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→65 Å / Num. obs: 13322 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1942 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLR

3glr


Resolution: 2.5→65 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 664 5 %RANDOM
Rwork0.20537 ---
obs0.20752 12653 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---1.04 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 11 68 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9923043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92222.81296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1815364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7111519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221698
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_it0.7071.51387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35622254
X-RAY DIFFRACTIONr_scbond_it1.9283848
X-RAY DIFFRACTIONr_scangle_it3.1814.5789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 40 -
Rwork0.278 937 -
obs-704 96.54 %

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