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- PDB-2h4j: Sir2-deacetylated peptide (from enzymatic turnover in crystal) -

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Basic information

Entry
Database: PDB / ID: 2h4j
TitleSir2-deacetylated peptide (from enzymatic turnover in crystal)
Components
  • Cellular tumor antigen p53
  • NAD-dependent deacetylase
KeywordsHYDROLASE / rossmann fold / Zn binding domain
Function / homology
Function and homology information


protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / 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 / histone deacetylase activity, NAD-dependent / 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 / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / negative regulation of DNA replication / 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 / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / NAD+ binding / hematopoietic stem cell differentiation / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / Pyroptosis / embryonic organ development / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / type II interferon-mediated signaling pathway / somitogenesis / cellular response to actinomycin D / core promoter sequence-specific DNA binding / cellular response to glucose starvation / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress / cardiac muscle cell apoptotic process / mitotic G1 DNA damage checkpoint signaling
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 ...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 / 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE / Cellular tumor antigen p53 / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHoff, K.G. / Avalos, J.L. / Sens, K. / Wolberger, C.
CitationJournal: Structure / Year: 2006
Title: Insights into the Sirtuin Mechanism from Ternary Complexes Containing NAD(+) and Acetylated Peptide.
Authors: Hoff, K.G. / Avalos, J.L. / Sens, K. / Wolberger, C.
History
DepositionMay 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,4575
Polymers29,6682
Non-polymers7893
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.049, 59.683, 107.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 2098.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: F-moc synthesized peptide / References: UniProt: P04637

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Non-polymers , 4 types, 77 molecules

#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


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Chemical ChemComp-OAD / 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE


Type: RNA linking / Mass: 601.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N5O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17933 / Num. obs: 16973 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.092 / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1yc5

1yc5


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.048 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 913 5.1 %RANDOM
Rwork0.19762 ---
obs0.19999 16973 99.94 %-
all-16886 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 49 74 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222020
X-RAY DIFFRACTIONr_angle_refined_deg1.7442.0162732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64524.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4041512
X-RAY DIFFRACTIONr_chiral_restr0.110.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021478
X-RAY DIFFRACTIONr_nbd_refined0.2270.2894
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21381
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.212
X-RAY DIFFRACTIONr_mcbond_it1.6121.51283
X-RAY DIFFRACTIONr_mcangle_it2.39421990
X-RAY DIFFRACTIONr_scbond_it4.393841
X-RAY DIFFRACTIONr_scangle_it4.7654.5742
X-RAY DIFFRACTIONr_rigid_bond_restr4.50332124
X-RAY DIFFRACTIONr_sphericity_free7.971375
X-RAY DIFFRACTIONr_sphericity_bonded3.34931985
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 71 -
Rwork0.21 1221 -
obs--100 %

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