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- PDB-1yc2: Sir2Af2-NAD-ADPribose-nicotinamide -

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Basic information

Entry
Database: PDB / ID: 1yc2
TitleSir2Af2-NAD-ADPribose-nicotinamide
ComponentsNAD-dependent deacetylase 2
KeywordsHYDROLASE / sir2 / sirtuin / nicotinamide / NAD / ADPribose / ternary complex
Function / homology
Function and homology information


protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding ...protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding / zinc ion binding / cytoplasm
Similarity search - Function
Sirtuin, class U / Sirtuin, class III / 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. ...Sirtuin, class U / Sirtuin, class III / 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
ADENOSINE-5-DIPHOSPHORIBOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICOTINAMIDE / TRIETHYLENE GLYCOL / NAD-dependent protein deacylase 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAvalos, J.L. / Bever, M.K. / Wolberger, C.
CitationJournal: Mol.Cell / Year: 2005
Title: Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme.
Authors: Avalos, J.L. / Bever, K.M. / Wolberger, C.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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 deacetylase 2
B: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
D: NAD-dependent deacetylase 2
E: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54243
Polymers142,6855
Non-polymers6,85738
Water4,486249
1
A: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,83210
Polymers28,5371
Non-polymers1,2959
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37612
Polymers28,5371
Non-polymers1,83911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0348
Polymers28,5371
Non-polymers1,4977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8948
Polymers28,5371
Non-polymers1,3577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4065
Polymers28,5371
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: NAD-dependent deacetylase 2
hetero molecules

A: NAD-dependent deacetylase 2
B: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,13638
Polymers114,1484
Non-polymers5,98834
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area19820 Å2
ΔGint-286 kcal/mol
Surface area40370 Å2
MethodPISA
7
A: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86618
Polymers57,0742
Non-polymers2,79216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-145 kcal/mol
Surface area22070 Å2
MethodPISA
8
B: NAD-dependent deacetylase 2
hetero molecules

D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27020
Polymers57,0742
Non-polymers3,19618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area8100 Å2
ΔGint-120 kcal/mol
Surface area22470 Å2
MethodPISA
9
A: NAD-dependent deacetylase 2
B: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,20822
Polymers57,0742
Non-polymers3,13420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-116 kcal/mol
Surface area22450 Å2
MethodPISA
10
C: NAD-dependent deacetylase 2
hetero molecules

D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,92816
Polymers57,0742
Non-polymers2,85414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area7330 Å2
ΔGint-93 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.122, 181.562, 79.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
NAD-dependent deacetylase 2 / Regulatory protein SIR2 homolog 2 / SIR2-Af2


Mass: 28537.006 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: npdA2 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: O30124, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 10 types, 287 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HEPES, ammonium sulfate, PEG400, nicotinamide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.099997 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: 2 CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.099997 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 59851 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.108 / Rsym value: 0.086 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.49 Å / % possible all: 82.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 3011 -RANDOM
Rwork0.2093 ---
all0.2122 59933 --
obs0.2118 59360 97.3 %-
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9745 0 415 249 10409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006476
X-RAY DIFFRACTIONc_angle_deg1.23416

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