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- PDB-8tgp: Crystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide -

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Basic information

Entry
Database: PDB / ID: 8tgp
TitleCrystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide
Components
  • H4K16(myristoyl) peptide
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsTRANSFERASE / Sirtuin Sirtuin-2 SIRT2 / GENE 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 / response to redox state / regulation of myelination / positive regulation of DNA binding / 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 / negative regulation of megakaryocyte differentiation / heterochromatin / protein localization to CENP-A containing chromatin / lipid catabolic process / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / cellular response to epinephrine stimulus / Deposition of new CENPA-containing nucleosomes at the centromere / substantia nigra development / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / negative regulation of autophagy / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / epigenetic regulation of gene expression / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / 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) / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / negative regulation of protein catabolic process / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / autophagy
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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain ...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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold
Similarity search - Domain/homology
MYRISTIC ACID / Histone H4 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsNicely, N.I. / Weiser, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentPC 61-21. United States
CitationJournal: Biochemistry / Year: 2023
Title: Effects of Dimerization on the Deacylase Activities of Human SIRT2.
Authors: Yang, J. / Nicely, N.I. / Weiser, B.P.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: H4K16(myristoyl) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2264
Polymers37,9322
Non-polymers2942
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.138, 76.995, 56.005
Angle α, β, γ (deg.)90.000, 97.890, 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 / NAD-dependent protein defatty-acylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 36532.039 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 (E. coli)
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide H4K16(myristoyl) peptide


Mass: 1399.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KGLGKGGA(K-MYR)RHRK / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M MES monohydrate pH 6.5 (NaOH), 20% w/v PEG 4,000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→45.01 Å / Num. obs: 29902 / % possible obs: 96 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.46 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.023 / Net I/σ(I): 25.5
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3 % / Num. unique obs: 1339 / CC1/2: 0.923 / CC star: 0.98 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→45.01 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.2429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 2000 7.39 %
Rwork0.1902 25073 -
obs0.1933 27073 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.58 Å2
Refinement stepCycle: LAST / Resolution: 1.76→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 16 78 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862307
X-RAY DIFFRACTIONf_angle_d0.99973102
X-RAY DIFFRACTIONf_chiral_restr0.0644336
X-RAY DIFFRACTIONf_plane_restr0.0083395
X-RAY DIFFRACTIONf_dihedral_angle_d10.652316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.355670.2926847X-RAY DIFFRACTION41.34
1.8-1.850.3255910.24621123X-RAY DIFFRACTION54.76
1.85-1.90.3051140.2271446X-RAY DIFFRACTION70.11
1.9-1.960.2561320.21371646X-RAY DIFFRACTION80.31
1.96-2.030.21911560.20061955X-RAY DIFFRACTION95.05
2.03-2.120.24121580.19751976X-RAY DIFFRACTION96.47
2.12-2.210.23281570.19411967X-RAY DIFFRACTION95.55
2.21-2.330.23921630.18562053X-RAY DIFFRACTION98.05
2.33-2.470.24261630.18432031X-RAY DIFFRACTION98.83
2.47-2.660.21521610.19122033X-RAY DIFFRACTION98.61
2.67-2.930.24171620.19562020X-RAY DIFFRACTION98.33
2.93-3.360.23211560.19811977X-RAY DIFFRACTION95.22
3.36-4.230.20661590.18191983X-RAY DIFFRACTION95.16
4.23-45.010.21411610.16732016X-RAY DIFFRACTION95.27
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)
12.825883132380.245548773749-0.2460680790740.9779119016790.4173129815472.17618171508-0.150476787866-0.314387069353-0.1495578449040.253726760963-0.146394221963-0.3410309229670.1409224958480.2873286306830.2088559268930.113618636996-0.0173683206528-0.04121532007890.1345658461190.05205978406380.188830834947-5.57114545349-14.57413548448.77702282745
20.182256163449-0.441383986277-0.1796556869821.116476601850.9951169485986.80801216538-0.07024130969430.67118773549-0.517337821713-0.203436606382-0.004717931139070.5138718680450.600176467418-0.8769586123960.04670882837330.311556944487-0.111039397173-0.03437563392520.734631843043-0.1271452410820.426198771361-17.6757271437-9.07838073076-23.6799100629
31.706378889160.0130652058543-0.4431023626812.051563567240.6376297774482.794561511430.08256257507850.08552322602490.0651804184148-0.372543176652-0.175905777543-0.373979965953-0.2863453397190.001386720629210.07847919432670.132905779426-0.0215298386950.02684902430430.0741751949830.02975794824990.15108238689-5.1971695964-3.64262045698-4.33500887421
42.033384702421.5108845877-1.028515564862.672120250010.01297802404777.98913273422-0.0257451708528-0.1570568640710.3505618346510.1177891628350.09563473133830.0792345298098-0.9992452862120.0182595600131-0.0586802014710.3540285736820.0260042123124-0.001488236239020.230794797537-0.006783931239340.145096321909-5.727682134631.71351356888-27.0818330377
50.4544519262860.0434390058217-0.5465942719461.32813820635-1.31136673361.87203394174-0.1414591982220.191198378645-0.322772716277-0.624994587138-0.232145319076-0.3205433092330.5564721902620.09073167859180.2439301295470.3075197562460.001716604159250.1016889348110.154608840376-0.009204495060080.261127326525-3.60825458777-16.5411565684-9.82456486036
61.93649371739-0.269779550002-0.0415997184952.49070165972-0.08741561659472.06954517855-0.0723132187776-0.00134587825672-0.487162507729-0.129080304894-0.1324456642630.1109134551730.525700426485-0.272529251682-0.09163968406290.137386763299-0.1053397230980.02717500934920.1061609728510.05180157598780.314586373563-12.6710286811-23.99475900223.42350403072
71.73973985619-0.4344559211590.3659356941646.02620971502-2.154419741273.229692392020.0956999241071-0.05905576713460.1183722820560.352118426992-0.115683476720.0767408276932-0.240210774149-0.1053588712660.01365898530540.0846951529062-0.01157579546850.01460489553220.108670817081-0.03428040384740.0868791770317-10.77905963311.928341067666.88160393427
82.65225189942.944106396712.071413173767.09380255076-1.573148602415.53752932345-0.1155706122690.073131901638-0.2172675935830.5402304310540.06861510325910.2538840331930.589640711881-0.3032171915920.05680756745820.9335600279290.0469885644520.05112368274830.5177135197-0.1768932840530.346793812449-10.2742613304-20.933634645-17.3973162632
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 57 through 91 )AA57 - 911 - 35
22chain 'A' and (resid 92 through 138 )AA92 - 13836 - 66
33chain 'A' and (resid 139 through 187 )AA139 - 18767 - 115
44chain 'A' and (resid 188 through 227 )AA188 - 227116 - 155
55chain 'A' and (resid 228 through 275 )AA228 - 275156 - 203
66chain 'A' and (resid 276 through 323 )AA276 - 323204 - 244
77chain 'A' and (resid 324 through 355 )AA324 - 355245 - 276
88chain 'B' and (resid 14 through 18 )BB14 - 181 - 5

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