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- PDB-4x3p: Sirt2 in complex with a myristoyl peptide -

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Basic information

Entry
Database: PDB / ID: 4x3p
TitleSirt2 in complex with a myristoyl peptide
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • peptide PRO-LYS-LYS-THR-GLY
KeywordsHYDROLASE/PEPTIDE / sirt2 / myristoyl peptide / 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 / 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 ...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 / tubulin deacetylation / paranodal junction / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / 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 / NAD-dependent protein lysine deacetylase activity / positive regulation of fatty acid biosynthetic process / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / myelination in peripheral nervous system / histone deacetylase activity, NAD-dependent / chromatin silencing complex / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / positive regulation of oocyte maturation / regulation of phosphorylation / juxtaparanode region of axon / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone deacetylase activity / histone acetyltransferase binding / positive regulation of DNA binding / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / glial cell projection / positive regulation of cell division / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / negative regulation of reactive oxygen species metabolic process / subtelomeric heterochromatin formation / heterochromatin / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / substantia nigra development / centriole / epigenetic regulation of gene expression / negative regulation of autophagy / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / heterochromatin formation / mitotic spindle / histone deacetylase binding / autophagy / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / cellular response to hypoxia / growth cone / midbody / perikaryon / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / 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 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tridecanethial / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, Y. / Zhang, W. / Hao, Q.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Deacylation Mechanism by SIRT2 Revealed in the 1'-SH-2'-O-Myristoyl Intermediate Structure.
Authors: Wang, Y. / Fung, Y.M.E. / Zhang, W. / He, B. / Chung, M.W.H. / Jin, J. / Hu, J. / Lin, H. / Hao, Q.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_type.id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: peptide PRO-LYS-LYS-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9416
Polymers34,9362
Non-polymers1,0044
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-12 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.606, 77.700, 56.473
Angle α, β, γ (deg.)90.00, 97.73, 90.00
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: 34404.691 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 52-355
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, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide peptide PRO-LYS-LYS-THR-GLY


Mass: 531.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 261 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#6: Chemical ChemComp-3LX / tridecanethial


Mass: 214.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M HEPES, 5% Glycerol / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29676 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Χ2: 0.895 / Net I/av σ(I): 19.298 / Net I/σ(I): 11.1 / Num. measured all: 109584
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.70.48929640.750.3020.5770.89100
1.86-1.943.70.36929440.840.2270.4350.92100
1.94-2.033.80.24929740.9290.1520.2930.91100
2.03-2.133.80.17329680.9560.1060.2040.911100
2.13-2.273.80.12829780.9730.0780.1510.90899.9
2.27-2.443.80.129890.9850.060.1170.90599.9
2.44-2.693.70.08329870.9880.0510.0980.98199.8
2.69-3.083.60.06629600.990.0410.0780.9899.8
3.08-3.883.60.04929680.9940.0310.0580.82799.2
3.88-503.50.04429440.9930.0280.0520.70296.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3O

4x3o


Resolution: 1.8→30.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.579 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.021 / Stereochemistry target values: 'MAXIMUM LIKELIHOOD'
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 1503 5.1 %RANDOM
Rwork0.154 ---
obs0.155 28100 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0.51 Å2
2--0 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 63 257 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022649
X-RAY DIFFRACTIONr_bond_other_d0.0070.022518
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.0023590
X-RAY DIFFRACTIONr_angle_other_deg1.3683.015851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2123.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15515469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8171516
X-RAY DIFFRACTIONr_chiral_restr0.2670.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212951
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02597
X-RAY DIFFRACTIONr_mcbond_it1.1371.7751270
X-RAY DIFFRACTIONr_mcbond_other1.1221.7731269
X-RAY DIFFRACTIONr_mcangle_it1.8982.6481603
LS refinement shellResolution: 1.799→1.846 Å
RfactorNum. reflection% reflection
Rfree0.122 91 -
Rwork0.098 1979 -
all-2070 -
obs--95.7 %
Refinement TLS params.Method: refined / Origin x: 5.727 Å / Origin y: 6.4177 Å / Origin z: 20.6755 Å
111213212223313233
T0.0282 Å2-0.009 Å2-0.004 Å2-0.0052 Å2-0.003 Å2--0.0189 Å2
L0.1809 °2-0.0021 °2-0.1305 °2-0.1927 °2-0.1646 °2--0.4494 °2
S0.0092 Å °0.0027 Å °-0.0519 Å °-0.0151 Å °-0.015 Å °0.027 Å °-0.0061 Å °0.0132 Å °0.0058 Å °

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