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- PDB-9vew: SIRT2 structure in complex with H3K18myr peptide and native NAD: ... -

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Basic information

Entry
Database: PDB / ID: 9vew
TitleSIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2
Components
  • Histone H3.1
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / deacetylase / cell cycle regulation / metabolic regulation
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 / histone deacetylase activity, NAD-dependent / positive regulation of oocyte maturation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / chromatin silencing complex / meiotic spindle / protein lysine deacetylase activity / response to redox state / regulation of myelination / 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 / Chromatin modifying enzymes / lipid catabolic process / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of autophagy / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ubiquitin binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / autophagy / Pre-NOTCH Transcription and Translation / spindle / histone deacetylase binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / mitotic spindle / structural constituent of chromatin / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome / heterochromatin formation / nucleosome assembly
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 / Histone H3 signature 1. / Histone H3 signature 2. ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
MYRISTIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZhang, N. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)0000-0001-9961-9046 China
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Structural basis of SIRT2 pre-catalysis NAD + binding dynamics and mechanism.
Authors: Zhang, N. / Pow, K.C. / Chen, L. / Hao, Q.
History
DepositionJun 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3638
Polymers35,1902
Non-polymers1,1736
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-5 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.919, 76.608, 55.707
Angle α, β, γ (deg.)90, 97.363, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#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: 34404.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 784.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 6 types, 38 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Tris 8.0, 25% PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.68→55.31 Å / Num. obs: 8852 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.995 / Net I/σ(I): 10.6
Reflection shellResolution: 2.68→2.81 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1158 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3O

4x3o


Resolution: 2.68→55.309 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.874 / SU B: 27.919 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R Free: 0.37
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2507 431 4.907 %
Rwork0.1823 8353 -
all0.186 --
obs-8784 98.069 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.752 Å2
Baniso -1Baniso -2Baniso -3
1--1.733 Å20 Å20.293 Å2
2--3.435 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.68→55.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 74 32 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162249
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.833303
X-RAY DIFFRACTIONr_angle_other_deg0.5591.7355220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7015307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.177513
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.6952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24110388
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9021092
X-RAY DIFFRACTIONr_chiral_restr0.070.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_nbd_refined0.2320.2600
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22206
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21180
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.26
X-RAY DIFFRACTIONr_nbd_other0.1770.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.25
X-RAY DIFFRACTIONr_mcbond_it1.9622.7161225
X-RAY DIFFRACTIONr_mcbond_other1.9622.7161225
X-RAY DIFFRACTIONr_mcangle_it3.1524.8641533
X-RAY DIFFRACTIONr_mcangle_other3.1514.8631534
X-RAY DIFFRACTIONr_scbond_it2.2352.9541214
X-RAY DIFFRACTIONr_scbond_other2.2342.9531215
X-RAY DIFFRACTIONr_scangle_it3.4555.3431770
X-RAY DIFFRACTIONr_scangle_other3.4545.3421771
X-RAY DIFFRACTIONr_lrange_it5.90527.1582783
X-RAY DIFFRACTIONr_lrange_other5.927.1552782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.68-2.750.316280.2266250.2316570.9380.96699.39120.207
2.75-2.8250.272250.2325930.2346230.9630.96999.19740.21
2.825-2.9060.316350.2086000.2136450.9470.97298.44960.188
2.906-2.9960.278290.195590.1945940.9450.97698.98990.174
2.996-3.0940.212210.1945670.1955900.970.97599.6610.175
3.094-3.2020.319320.2075340.2155740.9370.97298.60630.188
3.202-3.3220.275370.1964990.2015450.9480.97598.34860.182
3.322-3.4570.324210.1985030.2025280.940.97799.24240.182
3.457-3.610.214200.1674620.1685000.9770.98496.40.155
3.61-3.7860.278300.1694140.1754890.9520.98390.79750.164
3.786-3.990.21320.1624240.1654630.9720.98498.48810.157
3.99-4.230.206260.1674100.1694450.9780.98397.97750.167
4.23-4.520.188220.1413850.1434110.960.98899.02680.143
4.52-4.880.297170.1543480.1613750.940.98597.33330.158
4.88-5.3410.163100.1573420.1573560.9710.98598.87640.159
5.341-5.9650.329100.1973120.2023250.970.97799.07690.202
5.965-6.8740.32120.2152660.2192810.960.9798.93240.224
6.874-8.3870.18580.2052190.2042480.9840.97591.53230.221
8.387-11.7270.24780.1551790.1581880.940.98499.46810.174
11.727-55.3090.18780.2341120.231200.9820.9631000.267
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)
11.7102-0.1889-0.33632.2738-0.09643.2132-0.00950.169-0.0752-0.1883-0.00780.0645-0.0316-0.19450.01730.0207-0.0029-0.00730.0289-0.01610.11156.52256.344821.4107
22.29085.3511.333712.6543.32631.0757-0.013-0.26450.06110.1155-0.41730.41770.33160.02840.43030.65040.13720.21910.63240.11720.71795.9189-5.186410.1903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA52 - 606
2X-RAY DIFFRACTION2ALLC6 - 12

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