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- PDB-4bv3: CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 A... -

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Basic information

Entry
Database: PDB / ID: 4bv3
TitleCRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD
ComponentsNAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
KeywordsHYDROLASE / INHIBITOR
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 / 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 / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / 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 / 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 / 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
ADENOSINE-5-DIPHOSPHORIBOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NITRATE ION / Chem-OCZ / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGertz, M. / Nguyen, N.T.T. / Weyand, M. / Steegborn, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism
Authors: Gertz, M. / Fischer, F. / Nguyen, G.T.T. / Lakshminarasimhan, M. / Schutkowski, M. / Weyand, M. / Steegborn, C.
History
DepositionJun 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,32610
Polymers31,4841
Non-polymers1,8419
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.940, 63.380, 66.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL / HSIRT3 / REGULATORY PROTEIN SIR2 HOMOLOG 3 / SIR2-LIKE PROTEIN 3 / SIRT3


Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 116-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVFT3S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 9 types, 132 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-OCZ / (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide


Mass: 248.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13ClN2O
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMICROHETEROGENEITY BETWEEN BHOH 2095 AND AGLU 332, AND BAPR 1393 AND AHOH 2051
Sequence detailsCONSTRUCT COVERS RESIDUES 116 TO 399

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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: 2.03 Å3/Da / Density % sol: 39.55 % / Description: NONE
Crystal growDetails: 0.2 M (NH4)2SO4, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2011 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→45.8 Å / Num. obs: 17814 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GLT

3glt


Resolution: 2→45.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.019 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20942 891 5 %RANDOM
Rwork0.16308 ---
obs0.16544 16922 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 116 123 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192357
X-RAY DIFFRACTIONr_bond_other_d0.0010.022246
X-RAY DIFFRACTIONr_angle_refined_deg2.0092.0393236
X-RAY DIFFRACTIONr_angle_other_deg0.9753.0025170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4322.574101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16215367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231522
X-RAY DIFFRACTIONr_chiral_restr0.1130.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
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_it1.6221.8131098
X-RAY DIFFRACTIONr_mcbond_other1.6181.8111097
X-RAY DIFFRACTIONr_mcangle_it2.4132.7071376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2462.0981259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 62 -
Rwork0.211 1179 -
obs--95.54 %

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