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- PDB-6l66: Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD... -

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Basic information

Entry
Database: PDB / ID: 6l66
TitleSirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • PRO-ARG-LYS-GLN-LEU-ALA
KeywordsTRANSFERASE / Sirtuin / myristoylation
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 / 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 ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / 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 / regulation of exit from mitosis / paranode region of axon / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / negative regulation of peptidyl-threonine phosphorylation / myelination in peripheral nervous system / rDNA heterochromatin formation / histone deacetylase activity, NAD-dependent / regulation of phosphorylation / protein deacetylation / positive regulation of oocyte maturation / Initiation of Nuclear Envelope (NE) Reformation / juxtaparanode region of axon / 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 / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of execution phase of apoptosis / positive regulation of cell division / NAD+ binding / glial cell projection / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / cellular response to epinephrine stimulus / substantia nigra development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / negative regulation of autophagy / epigenetic regulation of gene expression / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / autophagy / spindle / histone deacetylase binding / mitotic spindle / heterochromatin formation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / growth cone / midbody / cellular response to oxidative stress / DNA-binding transcription factor binding / cellular response to hypoxia / perikaryon / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / regulation of cell cycle / innate immune response / cell division / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Similarity search - Domain/homology
tridecanethial / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.169 Å
AuthorsChen, L.F.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)HKU/C7037-14G Hong Kong
CitationJournal: To Be Published
Title: Sirtuin 2 protein with H3K18 myristoylated peptide
Authors: Chen, L.F.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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
C: PRO-ARG-LYS-GLN-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0615
Polymers35,1182
Non-polymers9433
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-15 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.480, 78.044, 56.236
Angle α, β, γ (deg.)90.000, 97.620, 90.000
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 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34403.707 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 K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase
#2: Protein/peptide PRO-ARG-LYS-GLN-LEU-ALA


Mass: 713.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 180 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Chemical ChemComp-3LX / tridecanethial


Mass: 214.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 6.5 / Details: 0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 17043 / % possible obs: 91 % / Redundancy: 3.3 % / CC1/2: 0.954 / Net I/σ(I): 5.67
Reflection shellResolution: 2.16→2.21 Å / Num. unique obs: 615 / CC1/2: 0.761

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3P

4x3p


Resolution: 2.169→37.149 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2339 683 4.9 %
Rwork0.1738 --
obs0.1767 13951 81.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.98 Å2 / Biso mean: 41.3592 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 2.169→37.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 59 177 2650
Biso mean--43.68 44.55 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082557
X-RAY DIFFRACTIONf_angle_d1.0213454
X-RAY DIFFRACTIONf_chiral_restr0.051374
X-RAY DIFFRACTIONf_plane_restr0.006436
X-RAY DIFFRACTIONf_dihedral_angle_d11.4682137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1695-2.3370.2984970.2189198661
2.337-2.57210.33031090.2139233873
2.5721-2.94420.28611370.2061260780
2.9442-3.70880.21751730.1782308795
3.7088-37.1490.20481670.149325099

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