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- PDB-2od9: Structural Basis for Nicotinamide Inhibition and Base Exchange in... -

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Basic information

Entry
Database: PDB / ID: 2od9
TitleStructural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes
Components
  • H4 peptide
  • NAD-dependent deacetylase HST2
KeywordsHYDROLASE / Zn binding protein / Rossmann fold
Function / homology
Function and homology information


negative regulation of mitotic recombination / NAD-dependent histone H4K16 deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ binding / transferase activity / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A1R / NICOTINAMIDE / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMarmorstein, R. / Sanders, B.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes.
Authors: Sanders, B.D. / Zhao, K. / Slama, J.T. / Marmorstein, R.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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
Revision 1.4Aug 30, 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 1.5Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1365
Polymers36,4062
Non-polymers7303
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-5 kcal/mol
Surface area13620 Å2
MethodPISA
2
A: NAD-dependent deacetylase HST2
B: H4 peptide
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)74,27110
Polymers72,8124
Non-polymers1,4606
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area7500 Å2
ΔGint-26 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.940, 105.940, 67.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit.

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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: 34794.828 Da / Num. of mol.: 1 / Fragment: Hst2 catalytic core domain, residues 1-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HST2 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 Bl-21 gold
References: UniProt: P53686, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide H4 peptide


Mass: 1610.925 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N6O12P2
#5: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 27580 / Num. obs: 27580 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.111 / Rsym value: 0.117 / Χ2: 1.288 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2735 / Rsym value: 0.276 / Χ2: 1.017 / % possible all: 99.6

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Phasing

Phasing MRRfactor: 0.389 / Cor.coef. Fo:Fc: 0.658 / Cor.coef. Io to Ic: 0.404
Highest resolutionLowest resolution
Rotation3 Å91.287 Å
Translation3 Å91.287 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SZD

1szd


Resolution: 2.05→28.34 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2636 8.9 %random
Rwork0.218 ---
all0.218 27580 --
obs0.245 26344 88.8 %-
Solvent computationBsol: 59.072 Å2
Displacement parametersBiso mean: 36.862 Å2
Baniso -1Baniso -2Baniso -3
1-7.01 Å23.07 Å20 Å2
2--7.01 Å20 Å2
3----14.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 45 116 2527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3HPD_nic.param
X-RAY DIFFRACTION4water_rep.param

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