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- PDB-3pki: Human SIRT6 crystal structure in complex with ADP ribose -

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Basic information

Entry
Database: PDB / ID: 3pki
TitleHuman SIRT6 crystal structure in complex with ADP ribose
ComponentsNAD-dependent deacetylase sirtuin-6
KeywordsHYDROLASE / SIRT6 / ADP ribose / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / ketone biosynthetic process / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / regulation of lipid catabolic process / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / chromosome, subtelomeric region ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / ketone biosynthetic process / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / regulation of lipid catabolic process / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / chromosome, subtelomeric region / pericentric heterochromatin formation / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / protein localization to site of double-strand break / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / NAD-dependent histone deacetylase activity / positive regulation of chondrocyte proliferation / positive regulation of telomere maintenance / protein deacetylation / negative regulation of glucose import / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of vascular endothelial cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / negative regulation of protein import into nucleus / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / negative regulation of transcription elongation by RNA polymerase II / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / subtelomeric heterochromatin formation / regulation of lipid metabolic process / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / NAD+ binding / positive regulation of fat cell differentiation / negative regulation of gluconeogenesis / pericentric heterochromatin / regulation of protein localization to plasma membrane / response to UV / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / base-excision repair / circadian regulation of gene expression / protein destabilization / regulation of circadian rhythm / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / 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 / 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 / Rossmann fold ...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 / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsPan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Min, J. / Edwards, A.M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and biochemical functions of SIRT6.
Authors: Pan, P.W. / Feldman, J.L. / Devries, M.K. / Dong, A. / Edwards, A.M. / Denu, J.M.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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-6
B: NAD-dependent deacetylase sirtuin-6
C: NAD-dependent deacetylase sirtuin-6
D: NAD-dependent deacetylase sirtuin-6
E: NAD-dependent deacetylase sirtuin-6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,59867
Polymers234,6406
Non-polymers5,95861
Water16,916939
1
A: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,21210
Polymers39,1071
Non-polymers1,1059
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,02012
Polymers39,1071
Non-polymers91311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,11614
Polymers39,1071
Non-polymers1,00913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0209
Polymers39,1071
Non-polymers9138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30811
Polymers39,1071
Non-polymers1,20110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,92411
Polymers39,1071
Non-polymers81710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: NAD-dependent deacetylase sirtuin-6
B: NAD-dependent deacetylase sirtuin-6
C: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,34736
Polymers117,3203
Non-polymers3,02733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-165 kcal/mol
Surface area35470 Å2
MethodPISA
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D: NAD-dependent deacetylase sirtuin-6
E: NAD-dependent deacetylase sirtuin-6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,25131
Polymers117,3203
Non-polymers2,93128
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-189 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.367, 90.200, 90.180
Angle α, β, γ (deg.)118.09, 91.39, 115.80
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 39106.707 Da / Num. of mol.: 6 / Mutation: K265E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODON(+) PRARE
References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 1000 molecules

#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 26 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: 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.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 297 K / pH: 5.8
Details: 2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 118501 / Num. obs: 118501 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 14.6
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5734 / Rsym value: 0.956 / % possible all: 97

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
MOLREPphasing
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K35

3k35


Resolution: 2.04→29.87 Å / Cor.coef. Fo:Fc: 0.9385 / Cor.coef. Fo:Fc free: 0.9221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 5783 5 %RANDOM
Rwork0.1827 ---
obs0.1842 115679 --
Displacement parametersBiso mean: 33.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.4528 Å25.9642 Å22.7355 Å2
2---1.1849 Å21.976 Å2
3---6.6377 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 2.04→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12761 0 363 939 14063
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01135161.5
X-RAY DIFFRACTIONt_angle_deg0.94184512
X-RAY DIFFRACTIONt_dihedral_angle_d45392
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2602
X-RAY DIFFRACTIONt_gen_planes19745
X-RAY DIFFRACTIONt_it1328220
X-RAY DIFFRACTIONt_nbd65
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion16.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion17665
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact160144
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2531 400 4.75 %
Rwork0.2233 8024 -
all0.2247 8424 -

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