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- PDB-9vg3: SIRT2 structure in complex with H3K18myr peptide: pre NAD binding... -

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Basic information

Entry
Database: PDB / ID: 9vg3
TitleSIRT2 structure in complex with H3K18myr peptide: pre NAD binding state
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 / 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 / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 12, 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

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)35,0936
Polymers34,6752
Non-polymers4184
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint5 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.508, 72.528, 53.921
Angle α, β, γ (deg.)90, 95.27, 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: 33961.223 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: 713.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 4 types, 58 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris 8.0, 25% PEG2000MME

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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: 2.15→53.751 Å / Num. obs: 14755 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 11.9
Reflection shellResolution: 2.15→2.21 Å / Num. unique obs: 1240 / CC1/2: 0.876

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Processing

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

4x3o


Resolution: 2.15→53.751 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 17.498 / SU ML: 0.218 / Cross valid method: FREE R-VALUE / ESU R: 0.321 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2511 739 5.018 %
Rwork0.1963 13989 -
all0.199 --
obs-14728 98.779 %
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: 47.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.939 Å2-0 Å20.346 Å2
2---0.407 Å2-0 Å2
3---3.227 Å2
Refinement stepCycle: LAST / Resolution: 2.15→53.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 24 54 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162256
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.8383250
X-RAY DIFFRACTIONr_angle_other_deg0.5281.7485234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.952515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9410399
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4641098
X-RAY DIFFRACTIONr_chiral_restr0.0690.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.2130.2500
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.22068
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21172
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.215
X-RAY DIFFRACTIONr_nbd_other0.2640.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.25
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2170.21
X-RAY DIFFRACTIONr_mcbond_it1.5113.2571207
X-RAY DIFFRACTIONr_mcbond_other1.513.2571207
X-RAY DIFFRACTIONr_mcangle_it2.1425.8451507
X-RAY DIFFRACTIONr_mcangle_other2.1425.8461508
X-RAY DIFFRACTIONr_scbond_it1.5373.4121201
X-RAY DIFFRACTIONr_scbond_other1.5363.4121202
X-RAY DIFFRACTIONr_scangle_it2.2746.2321743
X-RAY DIFFRACTIONr_scangle_other2.2746.2321744
X-RAY DIFFRACTIONr_lrange_it3.51433.082665
X-RAY DIFFRACTIONr_lrange_other3.51633.0772662
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
2.15-2.2060.348670.26410500.26811210.8940.95299.64320.252
2.206-2.2660.315430.2649920.26610420.9250.95599.32820.247
2.266-2.3320.311570.2269700.2310350.9340.96699.22710.208
2.332-2.4030.248390.2229610.22310100.9650.96899.00990.2
2.403-2.4820.271510.2389030.249710.960.96498.24920.215
2.482-2.5690.285390.238780.2329640.9260.96695.12450.207
2.569-2.6660.322450.2378640.2429100.940.96799.89010.218
2.666-2.7740.256440.2238230.2248670.9470.9711000.207
2.774-2.8970.387420.228050.2278530.9340.97299.29660.207
2.897-3.0380.303430.2077560.2128010.9590.97499.75030.199
3.038-3.2020.27440.2057330.2097830.9480.97499.23370.204
3.202-3.3950.263310.26860.2037230.9580.97699.17010.204
3.395-3.6290.283300.1836410.1876880.9550.97997.52910.191
3.629-3.9180.201370.1835800.1846370.970.97996.86030.195
3.918-4.290.207300.1625510.1645810.9790.9841000.185
4.29-4.7920.171280.1475150.1485430.9830.9861000.173
4.792-5.5260.16260.1774400.1764690.9850.98299.36030.202
5.526-6.750.285260.1983700.2044070.9560.97897.29730.231
6.75-9.4720.248130.2022880.2043140.9670.97495.85990.248
9.472-53.7510.34940.1731840.1771880.9890.9741000.207
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)
11.0967-0.23250.24531.9696-0.53221.8506-0.00240.099-0.0893-0.22280.06120.13660.0311-0.4377-0.05880.0427-0.0234-0.01260.1521-0.00150.01467.04569.015518.7889
27.18890.2664-1.75790.84811.41063.03130.04160.1194-0.1321-0.0841-0.0361-0.0164-0.1456-0.1148-0.00560.2136-0.019-0.0230.16310.01550.20415.7043-2.32834.5063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA57 - 404
2X-RAY DIFFRACTION2ALLC7 - 12

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