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- PDB-3zgv: Structure of human SIRT2 in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 3zgv
TitleStructure of human SIRT2 in complex with ADP-ribose
ComponentsNAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
KeywordsHYDROLASE
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 ...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 / 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 / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone deacetylase activity / histone acetyltransferase binding / positive regulation of execution phase of apoptosis / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / glial cell projection / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / 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 / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / 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 / 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 / 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
ACETATE ION / Chem-AR6 / TRIETHYLENE GLYCOL / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMoniot, S. / Steegborn, C.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal Structure Analysis of Human Sirt2 and its Adp-Ribose Complex
Authors: Moniot, S. / Schutkowski, M. / Steegborn, C.
History
DepositionDec 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 8, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

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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)75,19814
Polymers73,3522
Non-polymers1,84612
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-19.4 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.860, 77.980, 114.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.31185, 0.95013, -0.00179), (0.94717, -0.31073, 0.07943), (0.07491, -0.02647, -0.99684)
Vector: -23.11791, 30.93525, 27.3033)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36676.168 Da / Num. of mol.: 2 / Fragment: RESIDUES 34-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T3 / 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

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Non-polymers , 6 types, 288 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5.5
Details: 20% PEG 10 000, 100 MM AMMONIUM ACETATE, 100 MM BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.278
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.36
ReflectionResolution: 2.27→64.4 Å / Num. obs: 61556 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J8F

1j8f


Resolution: 2.27→64.422 Å / σ(F): 1.23 / Phase error: 25.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1883 3111 0.1 %
Rwork0.1495 --
obs0.1537 61556 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.1 Å2
Refinement stepCycle: LAST / Resolution: 2.27→64.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 114 276 5088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064952
X-RAY DIFFRACTIONf_angle_d0.9146690
X-RAY DIFFRACTIONf_dihedral_angle_d14.2731841
X-RAY DIFFRACTIONf_chiral_restr0.048730
X-RAY DIFFRACTIONf_plane_restr0.004845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2702-2.30930.28181580.24862914X-RAY DIFFRACTION95
2.3093-2.35130.23241590.23592975X-RAY DIFFRACTION95
2.3513-2.39650.25771550.23482914X-RAY DIFFRACTION95
2.3965-2.44550.22141580.21482971X-RAY DIFFRACTION95
2.4455-2.49860.2211580.20662897X-RAY DIFFRACTION95
2.4986-2.55670.25711540.19322959X-RAY DIFFRACTION95
2.5567-2.62070.24431520.18652943X-RAY DIFFRACTION95
2.6207-2.69150.23651590.19862959X-RAY DIFFRACTION94
2.6915-2.77070.23011520.17562930X-RAY DIFFRACTION95
2.7707-2.86020.22611520.172937X-RAY DIFFRACTION95
2.8602-2.96240.21141560.17052892X-RAY DIFFRACTION94
2.9624-3.0810.18791540.16612954X-RAY DIFFRACTION94
3.081-3.22120.2481570.15622955X-RAY DIFFRACTION94
3.2212-3.3910.15881570.14872914X-RAY DIFFRACTION94
3.391-3.60340.18851500.14262869X-RAY DIFFRACTION94
3.6034-3.88160.16281560.12932901X-RAY DIFFRACTION92
3.8816-4.27210.16251540.11372842X-RAY DIFFRACTION92
4.2721-4.88990.12011420.10332901X-RAY DIFFRACTION93
4.8899-6.15950.20361530.12052907X-RAY DIFFRACTION94
6.1595-55.11390.15711500.13052934X-RAY DIFFRACTION94
Refinement TLS params.

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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0184-0.0253-0.01610.01570.03220.0350.01090.1101-0.0212-0.0378-0.0001-0.0280.05630.0417-00.1274-0.01830.00450.187-0.02940.16691.138715.4607-6.5872
20.03270.0105-0.00620.0102-0.00170.02110.13960.07710.11160.01350.0588-0.0787-0.10640.05390.04580.2451-0.11010.06910.2413-0.06020.201313.716840.97490.3109
30.0441-0.0021-0.0190.0121-0.01540.02880.06710.0863-0.0036-0.0687-0.00790.0726-0.0683-0.05720.03580.10070.02350.00080.20950.00550.117-3.470826.8411-12.0707
40.0227-0.00550.01610.0171-0.0115-0.0020.22580.04440.0026-0.0461-0.00390.049-0.1352-0.02820.03780.39790.08210.16510.05030.00540.24121.246649.3777-2.3548
50.0118-0.0008-0.0010.0020.00350.01620.10430.00820.10680.00820.05020.05490.0616-0.06620.02050.09320.0590.01460.2432-0.02680.2095-9.611723.7697-0.919
6-0.00050.001-0.00570.00180.010100.062-0.0272-0.05680.0078-0.01540.06390.02780.037700.1279-0.01880.01530.1501-0.02120.14792.456418.87915.7713
70.01220.0365-0.00280.04260.05640.0439-0.01740.1382-0.21410.04490.0204-0.0681-0.0410.00630.00210.12890.01070.00060.2076-0.05350.12113.761215.1109-13.1449
80.0060.00220.00760.10110.050.08990.05830.01570.06540.16840.0350.08-0.03390.04120.07060.1725-0.02180.08830.1668-0.04610.2226-1.603230.780729.2537
9-0.00550.0012-0.01060.0212-0.0016-0.00060.0817-0.03420.0110.0972-0.0991-0.08380.03560.0398-0.01590.1532-0.0119-0.02020.2361-0.07270.136220.247129.518129.8986
100.0270.0346-0.02720.0161-0.03250.02990.1155-0.0162-0.05330.1430.02140.08720.06680.01780.04030.2289-0.0680.27060.10650.0564-0.4011-0.635621.236438.7268
110.034-0.00460.00340.0066-0.00690.0673-0.1646-0.0966-0.0357-0.0087-0.1468-0.0530.04430.0494-0.0390.25470.09810.01110.4550.16970.164325.092417.622433.0323
120.13020.10160.05440.2115-0.03410.21340.10380.12870.10520.2312-0.06340.1235-0.05190.02830.19040.2081-0.01580.08490.0825-0.01130.1688-4.808626.836929.4377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 57 THROUGH 102 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 103 THROUGH 146 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 147 THROUGH 187 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 188 THROUGH 240 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 241 THROUGH 260 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 261 THROUGH 306 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 307 THROUGH 355 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 55 THROUGH 120 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 121 THROUGH 146 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 147 THROUGH 187 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 188 THROUGH 227 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 228 THROUGH 355 )

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