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- PDB-2hjh: Crystal Structure of the Sir2 deacetylase -

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Basic information

Entry
Database: PDB / ID: 2hjh
TitleCrystal Structure of the Sir2 deacetylase
ComponentsNAD-dependent histone deacetylase SIR2
KeywordsHYDROLASE / protein / sirtuin / acetyl-adp-ribose / nicotinamide
Function / homology
Function and homology information


negative regulation of DNA amplification / RENT complex / regulation of DNA stability / NAD-dependent histone H3K14 deacetylase activity / Regulation of HSF1-mediated heat shock response / establishment of protein-containing complex localization to telomere / NAD-dependent histone H3K9 deacetylase activity / NAD-dependent histone H4K16 deacetylase activity / telomere tethering at nuclear periphery / negative regulation of DNA recombination ...negative regulation of DNA amplification / RENT complex / regulation of DNA stability / NAD-dependent histone H3K14 deacetylase activity / Regulation of HSF1-mediated heat shock response / establishment of protein-containing complex localization to telomere / NAD-dependent histone H3K9 deacetylase activity / NAD-dependent histone H4K16 deacetylase activity / telomere tethering at nuclear periphery / negative regulation of DNA recombination / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / chromatin silencing complex / regulatory ncRNA-mediated gene silencing / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / subtelomeric heterochromatin formation / NAD+ binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining / chromatin organization / transferase activity / chromosome, telomeric region / nucleolus / metal ion binding / nucleus
Similarity search - Function
NAD-dependent histone deacetylase Sir2, N-terminal / Protein of unknown function (DUF592) / 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 ...NAD-dependent histone deacetylase Sir2, N-terminal / Protein of unknown function (DUF592) / 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
NICOTINAMIDE / Chem-XYQ / NAD-dependent histone deacetylase SIR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHall, B.E. / Ellenberger, T.E.
CitationJournal: To be Published
Title: Autoregulation of the yeast Sir2 deacetylase by reaction and trapping of a pseudosubstrate motif in the active site
Authors: Hall, B.E. / Buchberger, J.R. / Gerber, S.A. / Ambrosio, A.L.B. / Gygi, S.P. / Filman, D. / Moazed, D. / Ellenberger, T.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent histone deacetylase SIR2
B: NAD-dependent histone deacetylase SIR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9788
Polymers81,4002
Non-polymers1,5786
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.353, 89.566, 94.510
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent histone deacetylase SIR2 / Regulatory protein SIR2 / Silent information regulator 2


Mass: 40699.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR2, MAR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P06700, 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-XYQ / (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE / ACETYL-RIBOSYL-ADP


Mass: 601.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N5O15P2
#4: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 6000, 100mM TRIS pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 12.6 / Number: 586119 / Rmerge(I) obs: 0.049 / Χ2: 1.04 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 139309 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.99509810.031.0414.2
3.163.9910010.0420.9454.3
2.763.1610010.0441.074.4
2.512.7610010.061.0584.3
2.332.5110010.0811.024.4
2.192.3310010.111.0344.4
2.082.1910010.1561.0334.3
1.992.0810010.241.0694.3
1.921.9999.910.3561.0564.2
1.851.9290.110.4321.0463.2
ReflectionResolution: 1.85→50 Å / Num. all: 139309 / Num. obs: 71108 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.049 / Χ2: 1.037 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.432 / Num. unique all: 12698 / Χ2: 1.046 / % possible all: 90.1

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se30.4970.4310.1760.546
2Se31.4960.3520.1680.0810.531
3Se30.0280.5190.0160.280.464
4Se34.970.4640.1360.0590.496
5Se31.2090.530.1330.0840.428
6Se51.7420.6410.2370.4010.559
7Se33.2040.1850.2370.1280.331
8Se45.220.6230.5180.0520.426
9Se40.5830.8250.8280.170.387
10Se41.1850.2340.9470.190.319
11Se600.5110.1980.4230.535
12Se41.7820.150.8410.3220.297
13Se29.5890.7250.9670.2770.218
14Se600.8090.3210.3550.516
15Se40.0940.5210.070.4950.186
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.54 / Reflection: 68895 / Reflection acentric: 66994 / Reflection centric: 1901
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.3-36.5970.940.950.830182785233
3.3-5.30.940.940.8195879176411
2.6-3.30.820.830.711195611591365
2.3-2.60.650.650.421201911702317
2-2.30.40.410.242100320578425
1.9-20.180.180.111131211162150

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.062 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3497 5.1 %RANDOM
Rwork0.171 ---
all0.173 69079 --
obs-69079 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.546 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.85 Å2
2---1.37 Å20 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 96 517 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0225363
X-RAY DIFFRACTIONr_bond_other_d0.0020.024855
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.987288
X-RAY DIFFRACTIONr_angle_other_deg1.113311342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375647
X-RAY DIFFRACTIONr_chiral_restr0.1440.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025821
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021073
X-RAY DIFFRACTIONr_nbd_refined0.2320.21133
X-RAY DIFFRACTIONr_nbd_other0.2510.25674
X-RAY DIFFRACTIONr_nbtor_other0.10.23016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2384
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.236
X-RAY DIFFRACTIONr_mcbond_it1.3161.53261
X-RAY DIFFRACTIONr_mcangle_it2.16125294
X-RAY DIFFRACTIONr_scbond_it3.78432102
X-RAY DIFFRACTIONr_scangle_it5.0274.51993
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.302 199
Rwork0.259 3671
obs-3870
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)
10.87560.12310.01321.5274-0.35771.21620.0229-0.01190.03980.06230.04450.1437-0.0322-0.1503-0.06740.06620.0174-0.01320.06790.00520.0107-10.605726.169291.2654
21.04620.3532-0.07391.3739-0.44921.6966-0.0065-0.0394-0.16250.0603-0.0091-0.1958-0.02930.21910.01570.07490.0186-0.01380.0591-0.00070.03714.708143.256781.619
31.7651-0.0493-0.17952.87230.77271.8151-0.05850.1425-0.3255-0.19920.0378-0.23260.01530.15330.02070.0088-0.01980.01320.0831-0.08220.0987-25.119829.99545.922
43.87580.4144-0.74060.82210.45582.40490.11490.2310.303-0.14850.04950.197-0.1836-0.2226-0.16440.08110.0106-0.02440.06320.01140.0826-49.920145.741357.1779
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA216 - 2258 - 17
21AA231 - 27623 - 68
31AA320 - 363112 - 155
41AA448 - 556240 - 348
52AA296 - 31988 - 111
62AA364 - 408156 - 200
72AA426 - 447218 - 239
83BB216 - 2258 - 17
93BB231 - 27023 - 62
103BB320 - 363112 - 155
113BB448 - 555240 - 347
124BB294 - 31986 - 111
134BB364 - 407156 - 199
144BB424 - 447216 - 239

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