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- PDB-4y6l: Human SIRT2 in complex with myristoylated peptide (H3K9myr) -

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Basic information

Entry
Database: PDB / ID: 4y6l
TitleHuman SIRT2 in complex with myristoylated peptide (H3K9myr)
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • peptide THR-ALA-ARG-MYK-SER-THR-GLY
KeywordsHYDROLASE/PEPTIDE / sirtuin / SIRT / NAD-dependent deacetylase / myristoylated lysine / HYDROLASE-PEPTIDE complex
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 / Chromatin modifying enzymes / lipid catabolic process / cellular response to epinephrine stimulus / substantia nigra development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of autophagy / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / ubiquitin binding / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / autophagy / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Transcriptional regulation of granulopoiesis / HCMV Early Events / mitotic spindle
Similarity search - Function
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / 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.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
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 THR-ALA-ARG-MYK-SER-THR-GLY
D: peptide THR-ALA-ARG-MYK-SER-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3966
Polymers68,2654
Non-polymers1312
Water9,404522
1
A: NAD-dependent protein deacetylase sirtuin-2
C: peptide THR-ALA-ARG-MYK-SER-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1983
Polymers34,1322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area13510 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-2
D: peptide THR-ALA-ARG-MYK-SER-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1983
Polymers34,1322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-7 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.102, 48.824, 97.147
Angle α, β, γ (deg.)101.05, 91.53, 112.07
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 52-356
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 THR-ALA-ARG-MYK-SER-THR-GLY


Mass: 931.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*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.: 522 / 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: 47.23 %
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: 79168 / % possible obs: 95.6 % / Redundancy: 3.9 % / Rsym value: 0.023 / Net I/σ(I): 38.5

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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: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.626 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23241 3849 4.9 %RANDOM
Rwork0.20712 ---
obs0.20832 74836 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.04 Å20.04 Å2
2--0 Å2-0.08 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 2 522 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194637
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9886226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49623.431204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26515829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6251532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213410
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_it0.6391.472248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1522.1912790
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6591.5932389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.81112.9217621
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
Rfree0.257 281 -
Rwork0.226 5369 -
obs--94.43 %

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