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- PDB-5fyq: Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide -

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Basic information

Entry
Database: PDB / ID: 5fyq
TitleSirt2 in complex with a 13-mer trifluoroacetylated Ran peptide
Components
  • NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
  • RAN AA 31-43
KeywordsHYDROLASE / SIRTUIN / KDAC / LYSINE-DEACETYLASE / LYSINE-ACETYLATION / GENETIC-CODE EXPANSION
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / RNA nuclear export complex / tubulin deacetylase activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / regulation of exit from mitosis / paranode region of axon / manchette / NAD-dependent protein lysine deacetylase activity / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / Regulation of cholesterol biosynthesis by SREBP (SREBF) / chromatin silencing complex / importin-alpha family protein binding / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / positive regulation of oocyte maturation / juxtaparanode region of axon / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein lysine deacetylase activity / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / meiotic spindle / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / response to redox state / regulation of myelination / DNA metabolic process / dynein intermediate chain binding / histone acetyltransferase binding / histone deacetylase activity / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / mitotic sister chromatid segregation / glial cell projection / positive regulation of cell division / spermatid development / ribosomal large subunit export from nucleus / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / sperm flagellum / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / ribosomal small subunit export from nucleus / heterochromatin / ribosomal subunit export from nucleus / heterochromatin formation / nuclear pore / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / protein export from nucleus / viral process / negative regulation of autophagy / mitotic spindle organization / G protein activity / meiotic cell cycle / ubiquitin binding / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / negative regulation of protein catabolic process / recycling endosome / mitotic spindle / autophagy / histone deacetylase binding / positive regulation of protein import into nucleus / spindle / protein import into nucleus / GDP binding / melanosome
Similarity search - Function
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / small GTPase Ran family profile. / Ran GTPase / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / small GTPase Ran family profile. / Ran GTPase / 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 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP-binding nuclear protein Ran / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKnyphausen, P. / de Boor, S. / Scislowski, L. / Extra, A. / Baldus, L. / Schacherl, M. / Baumann, U. / Neundorf, I. / Lammers, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Insights Into Lysine-Deacetylation of Natively Folded Substrate Proteins by Sirtuins.
Authors: Knyphausen, P. / De Boor, S. / Kuhlmann, N. / Scislowski, L. / Extra, A. / Baldus, L. / Schacherl, M. / Baumann, U. / Neundorf, I. / Lammers, M.
History
DepositionMar 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: RAN AA 31-43
D: RAN AA 31-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8368
Polymers83,5134
Non-polymers3234
Water3,171176
1
A: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
D: RAN AA 31-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9184
Polymers41,7562
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-64 kcal/mol
Surface area13870 Å2
MethodPISA
2
B: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
C: RAN AA 31-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9184
Polymers41,7562
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-57.9 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.948, 114.948, 206.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2 / REGULATORY PROTEIN SIR2 HOMOLOG 2 / SIR2-LIKE PROTEIN 2


Mass: 40160.746 Da / Num. of mol.: 2 / Fragment: 50-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: PGEX / 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 RAN AA 31-43


Mass: 1595.735 Da / Num. of mol.: 2 / Fragment: PART OF SWITCH I, RESIDUES 31-43 / Source method: obtained synthetically / Details: TRIFLUOROACETYLATED AT K37 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P62826
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.07 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5 2.0M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 10, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→56.61 Å / Num. obs: 16888 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 12 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L3O

4l3o


Resolution: 3→56.61 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.843 / SU B: 23.787 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27115 856 5.1 %RANDOM
Rwork0.23163 ---
obs0.23371 15978 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 3→56.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 12 176 4605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194516
X-RAY DIFFRACTIONr_bond_other_d0.0080.024317
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.986088
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0029963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98223.673196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43115776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214985
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021005
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_it2.5934.8562242
X-RAY DIFFRACTIONr_mcbond_other2.5884.8572241
X-RAY DIFFRACTIONr_mcangle_it4.4137.2612785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6654.9012274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 68 -
Rwork0.26 1135 -
obs--100 %

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