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- PDB-9s44: Human Histone Deacetylase SIRT2 -

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Basic information

Entry
Database: PDB / ID: 9s44
TitleHuman Histone Deacetylase SIRT2
ComponentsNAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Lysine deacetylase / NAD+-dependant enzyme / Histone modification / Epigenetics
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / peptidyl-lysine deacetylation / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / negative regulation of NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / paranode region of axon / regulation of exit from mitosis / positive regulation of fatty acid biosynthetic process / Schmidt-Lanterman incisure / negative regulation of peptidyl-threonine phosphorylation / NAD-dependent protein lysine deacetylase activity / regulation of phosphorylation / protein acetyllysine N-acetyltransferase / myelination in peripheral nervous system / rDNA heterochromatin formation / protein deacetylation / positive regulation of oocyte maturation / histone deacetylase activity, NAD-dependent / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / chromatin silencing complex / meiotic spindle / protein lysine deacetylase activity / regulation of myelination / response to redox state / positive regulation of DNA binding / histone deacetylase activity / histone acetyltransferase binding / negative regulation of fat cell differentiation / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / positive regulation of execution phase of apoptosis / glial cell projection / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / negative regulation of autophagy / epigenetic regulation of gene expression / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / autophagy / spindle / histone deacetylase binding / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heterochromatin formation / myelin sheath / chromosome / growth cone / cellular response to oxidative stress / midbody / perikaryon / cellular response to hypoxia / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / chromosome, telomeric region / regulation of cell cycle / innate immune response / cell division / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWirawan, R. / Frei, M. / Heider, A. / Papenkordt, N. / Friedrich, F. / Wein, T. / Jung, M. / Groll, M. / Huber, E.M. / Bracher, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)503267011 Germany
German Research Foundation (DFG)325871075 (SFB1309) Germany
CitationJournal: To Be Published
Title: Enhancing the potency of sirtuin 2 inhibitors through rational functional group modulations targeting NAD+ co-factor interactions
Authors: Wirawan, R. / Frei, M. / Heider, A. / Papenkordt, N. / Friedrich, F. / Wein, T. / Jung, M. / Groll, M. / Huber, E.M. / Bracher, F.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2432
Polymers34,1771
Non-polymers651
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.760, 73.510, 54.980
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / NAD-dependent protein defatty-acylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34177.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium formate 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 15167 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.2
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1942 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 19.267 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27373 758 5 %RANDOM
Rwork0.22844 ---
obs0.23064 14404 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.445 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å2-0.83 Å2
2--0.29 Å20 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 1 40 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152146
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6443047
X-RAY DIFFRACTIONr_angle_other_deg1.031.5794969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.28221.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08315405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5461515
X-RAY DIFFRACTIONr_chiral_restr0.0360.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
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_it1.1044.3971113
X-RAY DIFFRACTIONr_mcbond_other1.1044.3941112
X-RAY DIFFRACTIONr_mcangle_it1.6286.5811386
X-RAY DIFFRACTIONr_mcangle_other1.6276.5831387
X-RAY DIFFRACTIONr_scbond_it0.9064.651149
X-RAY DIFFRACTIONr_scbond_other0.9034.6481148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3116.9141661
X-RAY DIFFRACTIONr_long_range_B_refined2.45850.8782372
X-RAY DIFFRACTIONr_long_range_B_other2.4350.8912370
X-RAY DIFFRACTIONr_rigid_bond_restr0.24734408
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 57 -
Rwork0.325 1081 -
obs--98.61 %
Refinement TLS params.Method: refined / Origin x: -7.4508 Å / Origin y: -11.544 Å / Origin z: -7.4917 Å
111213212223313233
T0.0112 Å2-0.0198 Å20.0104 Å2-0.1308 Å20.0125 Å2--0.0202 Å2
L0.1034 °2-0.1116 °2-0.0466 °2-0.2705 °2-0.2406 °2--0.6226 °2
S-0.0166 Å °0.0549 Å °-0.0091 Å °-0.0094 Å °0.0566 Å °0.0172 Å °0.0378 Å °-0.272 Å °-0.04 Å °

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