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- PDB-5d7q: Crystal structure of human Sirt2 in complex with ADPR and CHIC35 -

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Basic information

Entry
Database: PDB / ID: 5d7q
TitleCrystal structure of human Sirt2 in complex with ADPR and CHIC35
ComponentsNAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Human Sirt2 / Inhibitor complex / Deacylase
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 / positive regulation of meiotic nuclear division / NAD-dependent histone H4K16 deacetylase activity / : / positive regulation of attachment of spindle microtubules to kinetochore / tubulin deacetylation / NAD-dependent protein demyristoylase activity ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / positive regulation of meiotic nuclear division / NAD-dependent histone H4K16 deacetylase activity / : / positive regulation of attachment of spindle microtubules to kinetochore / tubulin deacetylation / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / paranode region of axon / Schmidt-Lanterman incisure / regulation of exit from mitosis / myelination in peripheral nervous system / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / histone deacetylase activity / regulation of myelination / histone acetyltransferase binding / negative regulation of fat cell differentiation / positive regulation of execution phase of apoptosis / negative regulation of peptidyl-threonine phosphorylation / glial cell projection / subtelomeric heterochromatin formation / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / spindle / autophagy / histone deacetylase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / cellular response to oxidative stress / chromosome / midbody / growth cone / cellular response to hypoxia / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / centrosome / negative regulation of DNA-templated transcription / 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 / DHS-like NAD/FAD-binding domain superfamily ...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-4I5 / Chem-AR6 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationJu295/8-1 Germany
German Research FoundationSFB992 Medical Epigenetics, Project Z02 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Authors: Rumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,13410
Polymers68,8332
Non-polymers2,3008
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-19 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.340, 78.170, 114.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Fragment: UNP residues 56-356
Source method: isolated from a genetically manipulated source
Details: Gly1 originates from TEV cleavage site His2/Met3 originate from NdeI restriction site of the vector
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical
ChemComp-4I5 / (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide


Mass: 262.735 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15ClN2O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 18 % (w/v) PEG 10000, 0.1 M Bis-Tris / PH range: 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→46.23 Å / Num. obs: 46758 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.6
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.716

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D7O

5d7o


Resolution: 2.01→46.23 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.889 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22459 2349 5 %RANDOM
Rwork0.21097 ---
obs0.21166 44359 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.06 Å20 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 2.01→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 146 137 5058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195074
X-RAY DIFFRACTIONr_bond_other_d0.0060.024777
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9956871
X-RAY DIFFRACTIONr_angle_other_deg0.7843.00111053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.523.624218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16615876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8321530
X-RAY DIFFRACTIONr_chiral_restr0.0690.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021147
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_it1.3112.7632406
X-RAY DIFFRACTIONr_mcbond_other1.3112.7622405
X-RAY DIFFRACTIONr_mcangle_it2.1424.1373009
X-RAY DIFFRACTIONr_mcangle_other2.1434.1363006
X-RAY DIFFRACTIONr_scbond_it1.4123.0132668
X-RAY DIFFRACTIONr_scbond_other1.4093.0122667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3714.4343861
X-RAY DIFFRACTIONr_long_range_B_refined4.04622.2965658
X-RAY DIFFRACTIONr_long_range_B_other4.0322.2715628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 157 -
Rwork0.325 3183 -
obs--97.66 %
Refinement TLS params.

T33: 0.0258 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4915-0.1131-0.15140.0611-0.04920.36340.0272-0.01590.0074-0.03950.0234-0.00280.0121-0.0546-0.05060.08-0.01960.01680.01610.0042-8.0935-17.088124.264
20.15530.0147-0.00620.3992-0.32040.4285-0.0272-0.0983-0.0486-0.0230.06280.0569-0.03480.0295-0.03550.0336-0.00290.00760.11240.0456-6.2158-17.023760.0727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 354
2X-RAY DIFFRACTION2B56 - 354

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