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- PDB-1szd: Structural basis for nicotinamide cleavage and ADP-ribose transfe... -

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Basic information

Entry
Database: PDB / ID: 1szd
TitleStructural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases
Components
  • Histone H4 peptide
  • NAD-dependent deacetylase HST2
KeywordsGENE REGULATION / hst2 / Sir2 / Sirtuin / histone deacetylase / protein deacetylase
Function / homology
Function and homology information


negative regulation of mitotic recombination / HDMs demethylate histones / HATs acetylate histones / NAD-dependent histone H4K16 deacetylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity ...negative regulation of mitotic recombination / HDMs demethylate histones / HATs acetylate histones / NAD-dependent histone H4K16 deacetylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / NAD+ binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Histone H4 / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhao, K. / Harshaw, R. / Chai, X. / Marmorstein, R.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases.
Authors: Zhao, K. / Harshaw, R. / Chai, X. / Marmorstein, R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Structure and Autoregulation Of The Yeast Hst2 Homolog Of Sir2
Authors: Zhao, K. / Harshaw, R. / Chai, X. / Marmorstein, R.
#2: Journal: Structure / Year: 2003
Title: Structure Of The Yeast Hst2 Protein Deacetylase In Ternary Complex With 2'-O-Acetyl ADP Ribose and Histone Peptide
Authors: Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_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.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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent deacetylase HST2
B: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6108
Polymers34,6742
Non-polymers9366
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-24 kcal/mol
Surface area13640 Å2
MethodPISA
2
A: NAD-dependent deacetylase HST2
B: Histone H4 peptide
hetero molecules

A: NAD-dependent deacetylase HST2
B: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,22116
Polymers69,3484
Non-polymers1,87312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553-x,-x+y,-z-4/31
Buried area8350 Å2
ΔGint-62 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.383, 105.383, 66.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NAD-dependent deacetylase HST2 / Homologous to SIR2 protein 2


Mass: 33476.383 Da / Num. of mol.: 1 / Fragment: catalytic core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: hst2 (1-294) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Gold)
References: UniProt: P53686, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Histone H4 peptide


Mass: 1197.457 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide naturally occurs in Saccharomyces cerevisiae (baker's yeast).
References: UniProt: P02309

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Non-polymers , 5 types, 346 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Ammonium Sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2003
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 67216 / Num. obs: 67216 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 13 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.059 / Net I/σ(I): 36.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6325 / Rsym value: 0.437 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q1A

1q1a


Resolution: 1.5→28.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 236729.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1977 3.1 %RANDOM
Rwork0.214 ---
all0.225 67216 --
obs0.214 67216 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.6629 Å2 / ksol: 0.369871 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å2-1.66 Å20 Å2
2---3.71 Å20 Å2
3---7.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 56 340 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_mcbond_it2.911.5
X-RAY DIFFRACTIONc_mcangle_it3.962
X-RAY DIFFRACTIONc_scbond_it4.672
X-RAY DIFFRACTIONc_scangle_it6.472.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 293 3.2 %
Rwork0.327 8966 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4018_ADR.PARAM018_ADR.TOP

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