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- PDB-9vh0: SIRT2-H187A structure in complex with H3K18myr peptide and native NAD -

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Basic information

Entry
Database: PDB / ID: 9vh0
TitleSIRT2-H187A 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 / 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 / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / regulation of phosphorylation / 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 / glial cell projection / positive regulation of execution phase of apoptosis / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / Chromatin modifying enzymes / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / telomere organization / Interleukin-7 signaling / negative regulation of autophagy / RNA Polymerase I Promoter Opening / 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 / 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 / Meiotic recombination / 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 / myelin sheath
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 / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 16, 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
B: NAD-dependent protein deacetylase sirtuin-2
C: Histone H3.1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72910
Polymers69,8154
Non-polymers1,9146
Water72140
1
A: NAD-dependent protein deacetylase sirtuin-2
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8655
Polymers34,9072
Non-polymers9573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-9 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-2
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8655
Polymers34,9072
Non-polymers9573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-7 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.434, 48.13, 96.194
Angle α, β, γ (deg.)100.187, 91.579, 112.167
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: 34193.496 Da / Num. of mol.: 2 / Mutation: H187A
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 4 types, 46 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES 5.5, 9.2% PEG10000

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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 PILATUS3 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: 2.41→47.13 Å / Num. obs: 21638 / % possible obs: 92.1 % / Redundancy: 3.7 % / CC1/2: 0.995 / Net I/σ(I): 8.9
Reflection shellResolution: 2.41→2.5 Å / Num. unique obs: 2145 / CC1/2: 0.809

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3O

4x3o


Resolution: 2.41→47.129 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.313 / SU ML: 0.274 / Cross valid method: FREE R-VALUE / ESU R: 0.866 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2733 1083 5.009 %
Rwork0.1976 20539 -
all0.201 --
obs-21622 92.056 %
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: 46.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.979 Å20.71 Å2-2.658 Å2
2---0.164 Å2-4.357 Å2
3---3.359 Å2
Refinement stepCycle: LAST / Resolution: 2.41→47.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 120 40 4731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124816
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164465
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.846513
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7510357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7565586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.863530
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.84254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77310792
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.01610198
X-RAY DIFFRACTIONr_chiral_restr0.0770.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
X-RAY DIFFRACTIONr_nbd_refined0.220.21061
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.24245
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22315
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.223
X-RAY DIFFRACTIONr_nbd_other0.240.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2960.22
X-RAY DIFFRACTIONr_mcbond_it3.8944.5732359
X-RAY DIFFRACTIONr_mcbond_other3.8934.5732359
X-RAY DIFFRACTIONr_mcangle_it5.8898.2032940
X-RAY DIFFRACTIONr_mcangle_other5.8898.2052941
X-RAY DIFFRACTIONr_scbond_it3.9574.8622457
X-RAY DIFFRACTIONr_scbond_other3.9564.8632458
X-RAY DIFFRACTIONr_scangle_it6.168.8293573
X-RAY DIFFRACTIONr_scangle_other6.1598.833574
X-RAY DIFFRACTIONr_lrange_it8.80746.4695311
X-RAY DIFFRACTIONr_lrange_other8.80746.4755311
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
2.41-2.4730.39790.3213760.32417250.90.92284.34780.318
2.473-2.540.349680.26615280.26917010.9210.94193.82720.26
2.54-2.6130.333880.24714290.25215990.940.95494.87180.238
2.613-2.6940.331700.23614870.24116530.9240.9694.19240.225
2.694-2.7820.326660.24513500.24815020.9160.95994.27430.23
2.782-2.8790.252630.20913660.21115430.9550.97192.61180.194
2.879-2.9870.225650.18412330.18714230.9570.97891.21570.17
2.987-3.1090.261700.21111910.21413970.950.97290.26490.195
3.109-3.2460.322730.24110550.24713390.9350.9684.2420.224
3.246-3.4040.341730.24911380.25512730.8950.95895.12960.232
3.404-3.5870.31540.21210940.21711900.9460.97396.47060.198
3.587-3.8030.247520.17810400.18111500.9650.98194.95650.169
3.803-4.0640.236660.1559450.1610970.9690.98692.16040.148
4.064-4.3870.25330.1598800.1629990.9620.98591.39140.151
4.387-4.8010.251350.1537440.1579330.9610.98683.49410.148
4.801-5.3610.197360.1747860.1758470.9790.98597.04840.167
5.361-6.1770.273340.1816670.1857250.9710.98596.68970.174
6.177-7.5330.258270.1765630.1796230.9620.98494.7030.169
7.533-10.520.254140.1513980.1554820.9630.98885.47720.151
10.52-47.1290.203170.1992690.1992860.9810.9821000.198

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