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- PDB-3pkj: Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose -

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Basic information

Entry
Database: PDB / ID: 3pkj
TitleHuman SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose
ComponentsNAD-dependent deacetylase sirtuin-6
KeywordsHYDROLASE / ROSSMANN FOLD / ZN-BINDING DOMAIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ADP-RIBOSYLATION / 2'-N-Acetyl ADP ribose
Function / homology
Function and homology information


histone H3K56 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / regulation of lipid catabolic process / positive regulation of protein localization to chromatin ...histone H3K56 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / regulation of lipid catabolic process / positive regulation of protein localization to chromatin / NAD+-protein-arginine ADP-ribosyltransferase activity / DNA damage sensor activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / positive regulation of stem cell differentiation / negative regulation of D-glucose import across plasma membrane / positive regulation of chondrocyte proliferation / transposable element silencing / cardiac muscle cell differentiation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / pericentric heterochromatin formation / protein deacetylation / histone deacetylase activity, NAD-dependent / protein localization to site of double-strand break / positive regulation of blood vessel branching / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / TORC2 complex binding / positive regulation of vascular endothelial cell proliferation / histone deacetylase regulator activity / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / regulation of protein secretion / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / lncRNA binding / negative regulation of gene expression, epigenetic / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of stem cell population maintenance / positive regulation of telomere maintenance / negative regulation of cellular senescence / regulation of lipid metabolic process / site of DNA damage / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of transcription elongation by RNA polymerase II / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / negative regulation of gluconeogenesis / positive regulation of fat cell differentiation / subtelomeric heterochromatin formation / pericentric heterochromatin / response to UV / regulation of protein localization to plasma membrane / nucleosome binding / enzyme regulator activity / nucleotidyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / positive regulation of insulin secretion / base-excision repair / regulation of circadian rhythm / protein destabilization / chromatin DNA binding / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / protein import into nucleus / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / glucose homeostasis / positive regulation of cold-induced thermogenesis / site of double-strand break / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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-A2N / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsPan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Walker, J.R. / 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
Category: chem_comp_atom / chem_comp_bond ...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: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)239,78865
Polymers234,6406
Non-polymers5,14759
Water8,755486
1
A: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8697
Polymers39,1071
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,06111
Polymers39,1071
Non-polymers95410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86916
Polymers39,1071
Non-polymers76215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8697
Polymers39,1071
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,06110
Polymers39,1071
Non-polymers9549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,06114
Polymers39,1071
Non-polymers95413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: NAD-dependent deacetylase sirtuin-6
hetero molecules

D: NAD-dependent deacetylase sirtuin-6
hetero molecules

B: NAD-dependent deacetylase sirtuin-6
E: NAD-dependent deacetylase sirtuin-6
hetero molecules

A: NAD-dependent deacetylase sirtuin-6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,78865
Polymers234,6406
Non-polymers5,14759
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area16570 Å2
ΔGint-269 kcal/mol
Surface area64370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.042, 135.780, 89.105
Angle α, β, γ (deg.)90.00, 120.02, 90.00
Int Tables number4
Space group name H-MP1211

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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: K267E
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, 545 molecules

#2: Chemical
ChemComp-A2N / [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / 2'-N-Acetyl ADP ribose


Mass: 600.368 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H26N6O14P2
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 35 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 29, 2010 / Details: VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 100089 / Num. obs: 100089 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 35.52 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 15.9
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 2.02 / Num. unique all: 5012 / % possible all: 97.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
BUSTER2.8.0refinement
Coot0.6model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K35

3k35


Resolution: 2.12→20.5 Å / Cor.coef. Fo:Fc: 0.8585 / Cor.coef. Fo:Fc free: 0.8263 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 4924 4.94 %RANDOM
Rwork0.2341 ---
all0.2356 99730 --
obs0.2356 99730 --
Displacement parametersBiso mean: 35.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.7739 Å20 Å21.0382 Å2
2---5.9858 Å20 Å2
3---5.2119 Å2
Refine analyzeLuzzati coordinate error obs: 0.342 Å
Refinement stepCycle: LAST / Resolution: 2.12→20.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12367 0 335 486 13188
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01129611.5
X-RAY DIFFRACTIONt_angle_deg0.94177332
X-RAY DIFFRACTIONt_dihedral_angle_d41652
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2562
X-RAY DIFFRACTIONt_gen_planes19105
X-RAY DIFFRACTIONt_it1270920
X-RAY DIFFRACTIONt_nbd45
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion17.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion16885
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_contact145104
LS refinement shellResolution: 2.12→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 359 4.85 %
Rwork0.2554 7045 -
all0.2565 7404 -

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