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- PDB-4r8m: Human SIRT2 crystal structure in complex with BHJH-TM1 -

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Basic information

Entry
Database: PDB / ID: 4r8m
TitleHuman SIRT2 crystal structure in complex with BHJH-TM1
Components
  • BHJH-TM1 peptide
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Rossmann Fold / NAD-dependent protein deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex
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
tridecanethial / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTeng, Y.B. / Hao, Q. / Lin, H.N. / Jing, H.
CitationJournal: Sci Rep / Year: 2015
Title: Efficient Demyristoylase Activity of SIRT2 Revealed by Kinetic and Structural Studies
Authors: Teng, Y.B. / Jing, H. / Aramsangtienchai, P. / He, B. / Khan, S. / Hu, J. / Lin, H. / Hao, Q.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 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 / 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_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.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 / _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: BHJH-TM1 peptide
D: BHJH-TM1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9428
Polymers73,3834
Non-polymers5604
Water48627
1
A: NAD-dependent protein deacetylase sirtuin-2
C: BHJH-TM1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9714
Polymers36,6912
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-5 kcal/mol
Surface area13550 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-2
D: BHJH-TM1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9714
Polymers36,6912
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.936, 116.799, 70.905
Angle α, β, γ (deg.)90.00, 91.77, 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: 36159.715 Da / Num. of mol.: 2 / Fragment: rossmann fold, UNP residues 38-356
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 BHJH-TM1 peptide


Mass: 531.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-3LX / tridecanethial


Mass: 214.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THESE CHAIN_C AND CHAIN_D WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...THE SEQUENCE OF THESE CHAIN_C AND CHAIN_D WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE STRUCTURE IS TRUNCATED SIRTUIN-2 (38-356, GI:13775600).

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25%(v/v) PEG3350, 0.1M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2013
RadiationMonochromator: Be window / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 35229 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.921
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.385 / Rsym value: 0.062 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGO

3zgo


Resolution: 2.1→45.11 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 1727 5 %RANDOM
Rwork0.22091 ---
obs0.22353 32677 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å21.46 Å2
2---2.34 Å2-0 Å2
3---3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 30 27 4622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194722
X-RAY DIFFRACTIONr_bond_other_d00.024525
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9856368
X-RAY DIFFRACTIONr_angle_other_deg3.594310455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46523.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1871526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215221
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021053
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_it2.4324.4912331
X-RAY DIFFRACTIONr_mcbond_other2.434.492330
X-RAY DIFFRACTIONr_mcangle_it3.7226.7132905
X-RAY DIFFRACTIONr_mcangle_other3.7226.7142906
X-RAY DIFFRACTIONr_scbond_it2.8874.9322391
X-RAY DIFFRACTIONr_scbond_other2.8874.9322392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6897.2343464
X-RAY DIFFRACTIONr_long_range_B_refined6.42235.885125
X-RAY DIFFRACTIONr_long_range_B_other6.42235.8845124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 127 -
Rwork0.279 2419 -
obs--96.7 %

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