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- PDB-1yc5: Sir2-p53 peptide-nicotinamide -

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Basic information

Entry
Database: PDB / ID: 1yc5
TitleSir2-p53 peptide-nicotinamide
Components
  • Cellular tumor antigen p53 peptide
  • NAD-dependent deacetylase
KeywordsHYDROLASE / sir2 / sirtuin / sir2Tm / SirT1 / p53 / nicotinamide
Function / homology
Function and homology information


protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria ...protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / NAD+ binding / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress
Similarity search - Function
Sirtuin, class U / 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. / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...Sirtuin, class U / 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. / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / p53-like transcription factor, DNA-binding / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / Cellular tumor antigen p53 / Cellular tumor antigen p53 / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent deacetylase
B: Cellular tumor antigen p53 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8974
Polymers29,7092
Non-polymers1882
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.100, 59.749, 106.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27569.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: npdA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Cellular tumor antigen p53 peptide / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 2139.521 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q9NP68, UniProt: P04637*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: CHES, PEG3350, nicotinamide, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2004
RadiationMonochromator: 2 CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 58673 / Num. obs: 58321 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.053 / Rsym value: 0.046 / Net I/σ(I): 26.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5707 / Rsym value: 0.399 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.855 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20218 2903 5 %RANDOM
Rwork0.1854 ---
all0.1865 58595 --
obs0.18626 55273 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 10 266 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9792673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37224.30286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9571512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21392
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9471.51260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50821983
X-RAY DIFFRACTIONr_scbond_it2.3773800
X-RAY DIFFRACTIONr_scangle_it3.7484.5690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 232 -
Rwork0.231 3958 -
obs--98.96 %

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