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- PDB-4rmh: Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide -

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Basic information

Entry
Database: PDB / ID: 4rmh
TitleHuman Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide
Components
  • Ac-Lys-H3 peptide
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor 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 / paranodal junction ...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 / 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 / paranode region of axon / regulation of exit from mitosis / positive regulation of fatty acid biosynthetic process / Schmidt-Lanterman incisure / negative regulation of peptidyl-threonine phosphorylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / regulation of phosphorylation / myelination in peripheral nervous system / rDNA heterochromatin formation / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oocyte maturation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / chromatin silencing complex / meiotic spindle / protein lysine deacetylase activity / response to redox state / regulation of myelination / positive regulation of DNA binding / histone deacetylase activity / negative regulation of fat cell differentiation / histone acetyltransferase binding / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / positive regulation of execution phase of apoptosis / glial cell projection / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heterochromatin formation / myelin sheath / chromosome / growth cone / cellular response to oxidative stress / midbody / perikaryon / cellular response to hypoxia / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / 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 / cytoplasm / cytosol
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
Chem-3TE / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsRumpf, T. / Schiedel, M. / Karaman, B. / Roessler, C. / North, B.J. / Lehotzky, A. / Olah, J. / Ladwein, K.I. / Schmidtkunz, K. / Gajer, M. ...Rumpf, T. / Schiedel, M. / Karaman, B. / Roessler, C. / North, B.J. / Lehotzky, A. / Olah, J. / Ladwein, K.I. / Schmidtkunz, K. / Gajer, M. / Pannek, M. / Steegborn, C. / Sinclair, D.A. / Gerhardt, S. / Ovadi, J. / Schutkowski, M. / Sippl, W. / Einsle, O. / Jung, M.
CitationJournal: Nat Commun / Year: 2015
Title: Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.
Authors: Rumpf, T. / Schiedel, M. / Karaman, B. / Roessler, C. / North, B.J. / Lehotzky, A. / Olah, J. / Ladwein, K.I. / Schmidtkunz, K. / Gajer, M. / Pannek, M. / Steegborn, C. / Sinclair, D.A. / ...Authors: Rumpf, T. / Schiedel, M. / Karaman, B. / Roessler, C. / North, B.J. / Lehotzky, A. / Olah, J. / Ladwein, K.I. / Schmidtkunz, K. / Gajer, M. / Pannek, M. / Steegborn, C. / Sinclair, D.A. / Gerhardt, S. / Ovadi, J. / Schutkowski, M. / Sippl, W. / Einsle, O. / Jung, M.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

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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: Ac-Lys-H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6324
Polymers35,1462
Non-polymers4862
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-3 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.994, 73.302, 55.291
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34416.727 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-356
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 Ac-Lys-H3 peptide


Mass: 728.818 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-3TE / 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide


Mass: 420.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N4OS2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.8 M ammonium sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2013
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→55.06 Å / Num. obs: 53705 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5
Reflection shellResolution: 1.42→1.44 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→44.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.546 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18797 2658 5 %RANDOM
Rwork0.18066 ---
obs0.18103 51021 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.45 Å2
2--0.01 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.42→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 30 243 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192522
X-RAY DIFFRACTIONr_bond_other_d0.0020.022402
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9783422
X-RAY DIFFRACTIONr_angle_other_deg0.7983.0015563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19123.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4551518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
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_it1.0331.8111200
X-RAY DIFFRACTIONr_mcbond_other1.0331.8121201
X-RAY DIFFRACTIONr_mcangle_it1.7082.6961499
X-RAY DIFFRACTIONr_mcangle_other1.7082.6971500
X-RAY DIFFRACTIONr_scbond_it1.3192.061322
X-RAY DIFFRACTIONr_scbond_other1.3192.0611323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1473.0341909
X-RAY DIFFRACTIONr_long_range_B_refined4.17315.5563012
X-RAY DIFFRACTIONr_long_range_B_other4.02415.152892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 213 -
Rwork0.314 3760 -
all-3973 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 7.1921 Å / Origin y: 17.3393 Å / Origin z: 19.037 Å
111213212223313233
T0.0037 Å20.0047 Å20.0064 Å2-0.011 Å20.0022 Å2--0.0206 Å2
L0.0781 °2-0.0227 °2-0.0759 °2-0.1546 °2-0.0728 °2--0.1473 °2
S0.0005 Å °0.0201 Å °-0.0169 Å °0.0057 Å °0.0057 Å °0.0175 Å °-0.0097 Å °-0.0312 Å °-0.0062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 356
2X-RAY DIFFRACTION1A401

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