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- PDB-8xe7: Crystal structure of human Sirt2 without Sirt2-specific insertion -

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Basic information

Entry
Database: PDB / ID: 8xe7
TitleCrystal structure of human Sirt2 without Sirt2-specific insertion
ComponentsNAD-dependent protein deacetylase sirtuin-2
KeywordsMETAL BINDING PROTEIN / Deacetylation / Zn binding protein
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / : / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / : / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / Schmidt-Lanterman incisure / NAD-dependent protein lysine deacetylase activity / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone deacetylase activity / histone acetyltransferase binding / positive regulation of execution phase of apoptosis / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / glial cell projection / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / midbody / growth cone / cellular response to hypoxia / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / 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: 1.95 Å
AuthorsKonuma, T. / Akashi, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05720 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05774 Japan
Japan Society for the Promotion of Science (JSPS)21K19236 Japan
CitationJournal: Protein Sci. / Year: 2024
Title: Biophysical insights into the dimer formation of human Sirtuin 2.
Authors: Suzuki, N. / Konuma, T. / Ikegami, T. / Akashi, S.
History
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3072
Polymers33,2411
Non-polymers651
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.893, 69.208, 61.171
Angle α, β, γ (deg.)90.000, 99.341, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-2


Mass: 33241.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IXJ6
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris (pH6.0), PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.49 Å / Num. obs: 20867 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.47 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1049 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BALBESphasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8F

1j8f


Resolution: 1.95→45.49 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 1049 5.03 %
Rwork0.21 19809 -
obs0.2123 20858 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 1 138 2273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082185
X-RAY DIFFRACTIONf_angle_d1.06972967
X-RAY DIFFRACTIONf_chiral_restr0.0556335
X-RAY DIFFRACTIONf_plane_restr0.0073379
X-RAY DIFFRACTIONf_dihedral_angle_d11.8439300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.30441570.25122790X-RAY DIFFRACTION98.4
2.05-2.180.28981520.24572810X-RAY DIFFRACTION98.7
2.18-2.350.26071550.22822788X-RAY DIFFRACTION99.09
2.35-2.590.25731450.23832828X-RAY DIFFRACTION99.13
2.59-2.960.26841620.22542814X-RAY DIFFRACTION99.5
2.96-3.730.25741440.20882847X-RAY DIFFRACTION99.73
3.73-45.490.22851340.17792932X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.314797523616-0.0390196019082-0.01666295696130.3335028216950.1179227619460.3517663977550.0015545413896-0.350405253028-0.1652114833160.80024597016-0.1378318146550.0408317991440.882274446318-0.435938370169-0.071573244241.02182657209-0.3341255470890.1032078133120.477242356937-0.1249518526590.0255119158117.050490996893.4388720811428.8005827437
21.3111965139-0.2818705951960.396155445553.21033201611.115711605133.211817850560.397192856289-0.0374291497564-0.07278483778290.603391761942-0.206849433414-0.2235975104590.442818993892-0.273218317091-0.1209704817280.442503512179-0.136605298407-0.01316099246350.232390198443-0.0547166155130.25968590644512.8144384734-2.298928733110.188608078
32.082901341560.998125638615-0.6519200109341.874496858020.7695129619261.042928124030.03490623805020.16471280756-0.201315746768-0.2071321166790.180786877792-0.678322372474-0.1713529822960.27256236448-0.1986802020930.2191828431650.01528136373270.0221402681630.208438971112-0.04347276806680.34183641421124.3076057794-1.92577319082-13.4951617812
41.977724483130.228758118998-1.096906235181.05884630338-0.3528653976682.26961027770.01503859141670.0656738243573-0.4499916094960.818576871578-0.161328844591-0.0199740309931.11845560364-0.6375269563370.2330995436180.853546084981-0.2566468672680.02909886184250.288212393432-0.01892145237490.26615370720210.0534630161-11.88087785289.71059596596
51.357774704340.86008131660.1180448546192.606219852411.510814583362.0402961470.156027474501-0.0902158643608-0.06037500177070.145696293604-0.3384248839570.2161811863670.211972261145-0.4454485442910.1064796206120.119976117969-0.0307693210943-0.008447668544740.220108226945-0.03835095532560.2169381177548.14569331125-6.47084169344-7.06242768765
61.409466818990.141897605161-0.1774215824132.469402559852.445727349062.916994515270.250203715274-0.01109937504560.03204396391760.713655839181-0.3535987208310.09797808889770.5210337122-0.4294301074660.006392820210660.378147407125-0.08551063805450.02175462252080.290271707536-0.009432850392130.2163430521310.35658757035.0981580308615.4799086751
70.920288983668-0.242391899395-0.893094594960.1328911576070.03785520985661.219623161980.117343525506-0.184398862499-0.1112054187531.32267967654-0.349846482551-0.03906103343060.441428881773-0.228015685012-0.2053255872321.19355723475-0.254363656377-0.04533949496760.3051283114120.07223811078930.26028669077610.4992859157-20.197030016313.5799977257
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: AA1 / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 56 through 72 )56 - 721 - 17
22chain 'A' and (resid 73 through 102 )73 - 10218 - 44
33chain 'A' and (resid 103 through 138 )103 - 13845 - 80
44chain 'A' and (resid 139 through 157 )139 - 15781 - 99
55chain 'A' and (resid 158 through 240 )158 - 240100 - 182
66chain 'A' and (resid 241 through 337 )241 - 337183 - 264
77chain 'A' and (resid 338 through 355 )338 - 355265 - 282

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