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- PDB-9vgz: SIRT2-F96A structure in complex with H3K18myr peptide and native NAD -

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Basic information

Entry
Database: PDB / ID: 9vgz
TitleSIRT2-F96A structure in complex with H3K18myr peptide and native NAD
Components
  • Histone H3.1
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Deacylated / 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 / tubulin deacetylation / peptidyl-lysine deacetylation / lateral loop / NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / negative regulation of NLRP3 inflammasome complex assembly / paranode region of axon / regulation of exit from mitosis / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / 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 / histone deacetylase activity / regulation of myelination / response to redox state / positive regulation of DNA binding / negative regulation of fat cell differentiation / histone acetyltransferase binding / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / glial cell projection / positive regulation of execution phase of apoptosis / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / cellular response to epinephrine stimulus / substantia nigra development / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of autophagy / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / ubiquitin binding / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / negative regulation of protein catabolic process / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / autophagy / Pre-NOTCH Transcription and Translation / Meiotic recombination / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / mitotic spindle / structural constituent of chromatin / heterochromatin formation / nucleosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 domain / Histone-fold
Similarity search - Domain/homology
MYRISTIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsZhang, N. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2023B0303000003 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 15, 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
Revision 1.2Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)36,5267
Polymers35,4012
Non-polymers1,1255
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint2 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.915, 77.134, 56.155
Angle α, β, γ (deg.)90, 97.107, 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: 34615.906 Da / Num. of mol.: 1 / Mutation: F96A
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, 50 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / 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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→45.21 Å / Num. obs: 12400 / % possible obs: 91.2 % / Redundancy: 5.3 % / CC1/2: 0.995 / Net I/σ(I): 15.3
Reflection shellResolution: 2.34→2.42 Å / Num. unique obs: 1267 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9VEM

9vem


Resolution: 2.34→45.21 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.698 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.508 / ESU R Free: 0.265
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2356 567 4.581 %
Rwork0.1788 11810 -
all0.181 --
obs-12377 90.894 %
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: 43.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.209 Å20 Å22.402 Å2
2---0.756 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.34→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 71 45 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162295
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.8273391
X-RAY DIFFRACTIONr_angle_other_deg0.5721.7455329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.027515
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.24152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26810398
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.711095
X-RAY DIFFRACTIONr_chiral_restr0.0770.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined0.2270.2532
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.22202
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21255
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.283
X-RAY DIFFRACTIONr_metal_ion_refined0.1950.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.28
X-RAY DIFFRACTIONr_nbd_other0.2290.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.26
X-RAY DIFFRACTIONr_mcbond_it2.3723.0721254
X-RAY DIFFRACTIONr_mcbond_other2.373.0721254
X-RAY DIFFRACTIONr_mcangle_it3.4585.5021571
X-RAY DIFFRACTIONr_mcangle_other3.4575.5041572
X-RAY DIFFRACTIONr_scbond_it3.3933.4791248
X-RAY DIFFRACTIONr_scbond_other3.3923.4811249
X-RAY DIFFRACTIONr_scangle_it5.2056.2011820
X-RAY DIFFRACTIONr_scangle_other5.2036.2031821
X-RAY DIFFRACTIONr_lrange_it6.81131.3762792
X-RAY DIFFRACTIONr_lrange_other6.81131.3782792
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
2.34-2.4010.359450.1979130.2039850.9260.97997.25890.179
2.401-2.4660.301380.1949100.1989780.9440.97796.93250.174
2.466-2.5370.206330.1968920.1979500.9780.97797.36840.177
2.537-2.6150.313500.1968320.2039020.9460.97697.78270.175
2.615-2.7010.377240.2314910.2389210.9010.96955.91750.211
2.701-2.7950.321410.217860.2158440.9360.97297.98580.193
2.795-2.90.313360.2077850.2118360.9470.97398.20570.189
2.9-3.0180.325370.1997380.2067890.9340.97598.22560.183
3.018-3.1520.209350.1957350.1967890.9710.97697.59190.186
3.152-3.3050.244360.1816830.1847330.9590.97898.090.182
3.305-3.4820.259280.24530.2037100.9330.97367.74650.202
3.482-3.6920.252220.214490.2126670.9580.97570.61470.217
3.692-3.9450.247260.1884380.1926180.9650.97875.08090.207
3.945-4.2590.2180.1565600.1585890.9820.98598.13240.183
4.259-4.6610.197180.1295080.1315350.9810.9998.31780.15
4.661-5.2040.169240.1344600.1364890.9840.9998.97750.162
5.204-5.9960.159220.1584130.1584390.9870.98799.08880.185
5.996-7.3120.209180.1873470.1883680.9740.97999.18480.217
7.312-10.2080.161130.1432670.1442890.9870.98896.88580.185
10.208-45.210.1530.2231500.2221770.9970.96586.44070.372
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)
10.7576-0.1627-0.47120.8662-0.35062.5098-0.010.0549-0.0829-0.0860.00190.09150.0763-0.0890.00820.025-0.0137-0.02840.0553-0.02060.06946.10065.81220.6893
27.3104-5.5982-2.48514.62193.28646.6113-0.1892-0.05390.09240.17480.0611-0.0420.29110.13860.1280.2170.00230.0070.1656-0.01370.1717.7932-6.18678.422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA53 - 404
2X-RAY DIFFRACTION2ALLC6 - 12

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