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- PDB-6qcd: Human Sirt6 in complex with ADP-ribose and the activator quercetin -

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Basic information

Entry
Database: PDB / ID: 6qcd
TitleHuman Sirt6 in complex with ADP-ribose and the activator quercetin
ComponentsNAD-dependent protein deacetylase sirtuin-6
KeywordsHYDROLASE / Deacylase / Activator / Flavone / Allosteric / Isoform-selective
Function / homology
Function and homology information


ketone biosynthetic process / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / DNA damage sensor activity ...ketone biosynthetic process / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / DNA damage sensor activity / positive regulation of stem cell differentiation / NAD-dependent protein lysine deacetylase activity / positive regulation of chondrocyte proliferation / transposable element silencing / cardiac muscle cell differentiation / 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 / pericentric heterochromatin formation / histone deacetylase activity, NAD-dependent / protein deacetylation / negative regulation of D-glucose import / protein localization to site of double-strand break / positive regulation of blood vessel branching / histone H3K9 deacetylase activity, hydrolytic mechanism / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / positive regulation of vascular endothelial cell proliferation / TORC2 complex binding / histone deacetylase regulator activity / regulation of double-strand break repair via homologous recombination / negative regulation of protein import into nucleus / positive regulation of double-strand break repair / lncRNA binding / regulation of protein secretion / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of telomere maintenance / negative regulation of transcription elongation by RNA polymerase II / site of DNA damage / regulation of lipid metabolic process / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of cellular senescence / NAD+ binding / positive regulation of fat cell differentiation / negative regulation of gluconeogenesis / subtelomeric heterochromatin formation / pericentric heterochromatin / regulation of protein localization to plasma membrane / response to UV / nucleosome binding / enzyme regulator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / regulation of circadian rhythm / protein destabilization / base-excision repair / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / protein import into nucleus / transcription corepressor activity / glucose homeostasis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / site of double-strand break / positive regulation of cold-induced thermogenesis / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Rubrerythrin, domain 2 - #200 / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / Rubrerythrin, domain 2 / DHS-like NAD/FAD-binding domain superfamily / Single Sheet ...Rubrerythrin, domain 2 - #200 / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / Rubrerythrin, domain 2 / DHS-like NAD/FAD-binding domain superfamily / Single Sheet / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / TRIETHYLENE GLYCOL / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsYou, W. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis for the activation and inhibition of Sirtuin 6 by quercetin and its derivatives.
Authors: You, W. / Zheng, W. / Weiss, S. / Chua, K.F. / Steegborn, C.
History
DepositionDec 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-6
B: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,45021
Polymers67,2632
Non-polymers3,18719
Water6,215345
1
A: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,35712
Polymers33,6321
Non-polymers1,72611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0939
Polymers33,6321
Non-polymers1,4618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.366, 91.366, 143.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

21B-653-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NAD-dependent protein deacetylase sirtuin-6 / Regulatory protein SIR2 homolog 6 / SIR2-like protein 6


Mass: 33631.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Plasmid: pET151-D-TOPO / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 (DE3) pLysS
References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 8 types, 364 molecules

#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
PH range: 5.7-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.84→47.98 Å / Num. obs: 58932 / % possible obs: 99.7 % / Observed criterion σ(I): 1.12 / Redundancy: 6.9 % / Biso Wilson estimate: 37.47 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 9411 / CC1/2: 0.479 / Rrim(I) all: 1.76 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MF6

5mf6


Resolution: 1.84→45.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.739 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2100 3.6 %RANDOM
Rwork0.1682 ---
obs0.16944 56832 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--9.9 Å2-0 Å2-0 Å2
2---9.9 Å2-0 Å2
3---19.8 Å2
Refinement stepCycle: 1 / Resolution: 1.84→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 194 345 4905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174382
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6576360
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5810138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85719.795244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21415775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4111550
X-RAY DIFFRACTIONr_chiral_restr0.1020.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02980
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_it3.553.5552240
X-RAY DIFFRACTIONr_mcbond_other3.5473.5532239
X-RAY DIFFRACTIONr_mcangle_it4.4565.3092795
X-RAY DIFFRACTIONr_mcangle_other4.4565.3112796
X-RAY DIFFRACTIONr_scbond_it4.7814.1682439
X-RAY DIFFRACTIONr_scbond_other4.784.1692440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7426.043562
X-RAY DIFFRACTIONr_long_range_B_refined8.71243.1185153
X-RAY DIFFRACTIONr_long_range_B_other8.70443.0385132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.838→1.886 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 150 -
Rwork0.295 4057 -
obs--96.71 %

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