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- PDB-4iao: Crystal structure of Sir2 C543S mutant in complex with SID domain... -

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Basic information

Entry
Database: PDB / ID: 4iao
TitleCrystal structure of Sir2 C543S mutant in complex with SID domain of Sir4
Components
  • NAD-dependent histone deacetylase SIR2
  • Regulatory protein SIR4
KeywordsHYDROLASE/TRANSCRIPTION / protein complex / SIR2 / deacetylase / nucleus / HYDROLASE-TRANSCRIPTION complex
Function / homology
Function and homology information


negative regulation of DNA amplification / RENT complex / regulation of DNA stability / NAD-dependent histone H3K14 deacetylase activity / establishment of protein-containing complex localization to telomere / NAD-dependent histone H3K9 deacetylase activity / NAD-dependent histone H4K16 deacetylase activity / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery / rDNA heterochromatin ...negative regulation of DNA amplification / RENT complex / regulation of DNA stability / NAD-dependent histone H3K14 deacetylase activity / establishment of protein-containing complex localization to telomere / NAD-dependent histone H3K9 deacetylase activity / NAD-dependent histone H4K16 deacetylase activity / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery / rDNA heterochromatin / negative regulation of DNA recombination / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / regulatory ncRNA-mediated gene silencing / chromatin silencing complex / NAD-dependent histone deacetylase activity / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / nuclear inner membrane / negative regulation of DNA replication / positive regulation of heterochromatin formation / NAD+ binding / subtelomeric heterochromatin formation / heterochromatin / heterochromatin formation / nucleosome binding / double-strand break repair via nonhomologous end joining / transcription corepressor activity / chromatin organization / transferase activity / double-stranded DNA binding / chromosome, telomeric region / molecular adaptor activity / nucleolus / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1710 / Helix Hairpins - #1820 / NAD-dependent histone deacetylase Sir2, N-terminal / Protein of unknown function (DUF592) / Sir4, SID domain / Sir4 SID domain / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1710 / Helix Hairpins - #1820 / NAD-dependent histone deacetylase Sir2, N-terminal / Protein of unknown function (DUF592) / Sir4, SID domain / Sir4 SID domain / 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 / Helix Hairpins / DHS-like NAD/FAD-binding domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / NAD-dependent histone deacetylase SIR2 / Regulatory protein SIR4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.901 Å
AuthorsHsu, H.C. / Wang, C.L. / Wang, M. / Yang, N. / Chen, Z. / Sternglanz, R. / Xu, R.M.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding
Authors: Hsu, H.C. / Wang, C.L. / Wang, M. / Yang, N. / Chen, Z. / Sternglanz, R. / Xu, R.M.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 20, 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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 histone deacetylase SIR2
B: NAD-dependent histone deacetylase SIR2
C: Regulatory protein SIR4
D: Regulatory protein SIR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7078
Polymers147,4574
Non-polymers1,2494
Water1,982110
1
A: NAD-dependent histone deacetylase SIR2
C: Regulatory protein SIR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3534
Polymers73,7292
Non-polymers6252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-48 kcal/mol
Surface area24770 Å2
MethodPISA
2
B: NAD-dependent histone deacetylase SIR2
D: Regulatory protein SIR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3534
Polymers73,7292
Non-polymers6252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-49 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.406, 178.752, 121.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and ((resseq 129:154) or (resseq 163:186) or (resseq...
21chain B and ((resseq 129:154) or (resseq 163:186) or (resseq...
12chain C and ((resseq 812:823) or (resseq 830:876) or (resseq 882:890))
22chain D and ((resseq 812:823) or (resseq 830:876) or (resseq 882:890))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and ((resseq 129:154) or (resseq 163:186) or (resseq...
211chain B and ((resseq 129:154) or (resseq 163:186) or (resseq...
112chain C and ((resseq 812:823) or (resseq 830:876) or (resseq 882:890))
212chain D and ((resseq 812:823) or (resseq 830:876) or (resseq 882:890))

NCS ensembles :
ID
1
2

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Components

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


Mass: 55683.973 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 87-562 / Mutation: C543S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR2, MAR1, YDL042C, D2714 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06700, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein Regulatory protein SIR4 / Silent information regulator 4


Mass: 18044.748 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 737-893
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11978
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM sodium phosphate, 0.6M sodium citrate, 2mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.08
SYNCHROTRONNSLS X29A20.9790, 0.9794, 0.9600
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDApr 26, 2008
ADSC QUANTUM 4r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
20.9791
30.97941
40.961
ReflectionResolution: 2.9→50 Å / Num. all: 40373 / Num. obs: 36438 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 74.36 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.9 / % possible all: 76.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.901→36.431 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6781 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 36.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 1811 5 %
Rwork0.2267 --
obs0.2288 36243 89.66 %
all-40373 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.821 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 177.15 Å2 / Biso mean: 79.2548 Å2 / Biso min: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.4627 Å2-0 Å20 Å2
2---21.1136 Å2-0 Å2
3---30.4414 Å2
Refinement stepCycle: LAST / Resolution: 2.901→36.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8470 0 74 110 8654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058749
X-RAY DIFFRACTIONf_angle_d0.99911852
X-RAY DIFFRACTIONf_dihedral_angle_d14.5283278
X-RAY DIFFRACTIONf_chiral_restr0.0791319
X-RAY DIFFRACTIONf_plane_restr0.0051485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2822X-RAY DIFFRACTIONPOSITIONAL0.059
12B2822X-RAY DIFFRACTIONPOSITIONAL0.059
21C548X-RAY DIFFRACTIONPOSITIONAL0.045
22D548X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9009-3.00450.45861720.38972787295974
3.0045-3.12480.36351710.33353273344486
3.1248-3.26690.32231730.27613420359390
3.2669-3.4390.32791760.25383490366691
3.439-3.65430.26361750.2343439361491
3.6543-3.93610.27121950.21153487368291
3.9361-4.33170.24481780.20483459363790
4.3317-4.95710.21811980.18623472367091
4.9571-6.24030.2471740.21793665383994
6.2403-36.43340.26281990.21763940413998

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