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- PDB-4y6o: Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) -

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Basic information

Entry
Database: PDB / ID: 4y6o
TitleHuman SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
KeywordsHYDROLASE/PEPTIDE / sirtuin / SIRT / NAD-dependent deacetylase / myristoylated lysine / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production ...negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / negative regulation of striated muscle tissue development / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of satellite cell differentiation / negative regulation of protein-containing complex disassembly / response to 3,3',5-triiodo-L-thyronine / positive regulation of attachment of spindle microtubules to kinetochore / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of meiotic nuclear division / positive regulation of hair follicle development / negative regulation of myelination / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / negative regulation of bicellular tight junction assembly / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / paranodal junction / : / negative regulation of amyloid-beta clearance / peptidyl-lysine deacetylation / tubulin deacetylation / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / lateral loop / death receptor agonist activity / positive regulation of protein transport / NLRP3 inflammasome complex assembly / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / toll-like receptor 3 signaling pathway / embryonic digestive tract development / tubulin deacetylase activity / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / regulation of exit from mitosis / paranode region of axon / necroptotic signaling pathway / response to fructose / Schmidt-Lanterman incisure / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / leukocyte tethering or rolling / positive regulation of calcineurin-NFAT signaling cascade / protein acetyllysine N-acetyltransferase / negative regulation of peptidyl-threonine phosphorylation / 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 / myelination in peripheral nervous system / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / rDNA heterochromatin formation / cellular response to toxic substance / regulation of establishment of endothelial barrier / regulation of phosphorylation / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of oocyte maturation / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / chromatin silencing complex / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion
Similarity search - Function
Tumour necrosis factor alpha / Tumour necrosis factor / Sirtuin, class I / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / SIR2/SIRT2 'Small Domain' ...Tumour necrosis factor alpha / Tumour necrosis factor / Sirtuin, class I / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Tumour necrosis factor-like domain superfamily / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tumor necrosis factor / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKudo, N. / Ito, A. / Yoshida, M.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Authors: Feldman, J.L. / Dittenhafer-Reed, K.E. / Kudo, N. / Thelen, J.N. / Ito, A. / Yoshida, M. / Denu, J.M.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
D: peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3566
Polymers68,2254
Non-polymers1312
Water7,638424
1
A: NAD-dependent protein deacetylase sirtuin-2
C: peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1783
Polymers34,1122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area13420 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-2
D: peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1783
Polymers34,1122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.136, 48.785, 96.960
Angle α, β, γ (deg.)101.07, 91.33, 112.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 33201.223 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 52-291, 304-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: pGEX-4T3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide peptide LEU-PRO-LYS-MYK-THR-GLY-GLY


Mass: 911.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01375*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 77514 / % possible obs: 95.7 % / Redundancy: 1.9 % / Rsym value: 0.049 / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8F, 3ZGO

1j8f

3zgo


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.827 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23457 3770 4.9 %RANDOM
Rwork0.20631 ---
obs0.20769 73362 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.931 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.02 Å2-0.01 Å2
2---0.04 Å2-0.13 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 2 424 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9916255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11323.498203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5511530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6291.5672260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1292.3372805
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6621.7012399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.82313.5537529
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 251 -
Rwork0.247 4896 -
obs--85.48 %

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