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- PDB-5ol0: Structure of Leishmania infantum Silent Information Regulator 2 r... -

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Basic information

Entry
Database: PDB / ID: 5ol0
TitleStructure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide
Components
  • Cellular tumor antigen p53
  • Putative silent information regulator 2,Putative silent information regulator 2
KeywordsHYDROLASE / NAD-dependent histone deacetylase
Function / homology
Function and homology information


protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / negative regulation of helicase 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 / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria ...protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / negative regulation of helicase 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 / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / circadian behavior / cellular response to actinomycin D / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / glycosyltransferase activity / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / replicative senescence / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / viral process / positive regulation of intrinsic apoptotic signaling pathway / NAD+ binding / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of fibroblast proliferation / general transcription initiation factor binding / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / response to gamma radiation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / molecular function activator activity / transcription initiation-coupled chromatin remodeling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / autophagy / TP53 Regulates Transcription of DNA Repair Genes / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / promoter-specific chromatin binding / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / cellular response to gamma radiation / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / PML body / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKR-mediated signaling / Oncogene Induced Senescence / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular senescence / DNA Damage/Telomere Stress Induced Senescence
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. / Cellular tumor antigen p53, transactivation domain 2 ...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. / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / TPP-binding domain / : / 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 / p53-like transcription factor, DNA-binding / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRonin, C. / Ciesielski, F. / Ciapetti, P.
Funding support France, 1items
OrganizationGrant numberCountry
European Union602773 France
CitationJournal: PLoS ONE / Year: 2018
Title: The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design.
Authors: Ronin, C. / Costa, D.M. / Tavares, J. / Faria, J. / Ciesielski, F. / Ciapetti, P. / Smith, T.K. / MacDougall, J. / Cordeiro-da-Silva, A. / Pemberton, I.K.
History
DepositionJul 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative silent information regulator 2,Putative silent information regulator 2
B: Putative silent information regulator 2,Putative silent information regulator 2
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1566
Polymers75,0254
Non-polymers1312
Water4,306239
1
A: Putative silent information regulator 2,Putative silent information regulator 2
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5783
Polymers37,5132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area13790 Å2
MethodPISA
2
B: Putative silent information regulator 2,Putative silent information regulator 2
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5783
Polymers37,5132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 65.670, 66.620
Angle α, β, γ (deg.)90.00, 97.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative silent information regulator 2,Putative silent information regulator 2 / SIR2-like protein


Mass: 35373.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Compared to Uniprot sequence Q8I6E4, region P253-E300 was deleted from expressed sequence
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: SIR2RP1, LINJ_26_0200 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8I6E4, NAD+-protein-arginine ADP-ribosyltransferase
#2: Protein/peptide Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 2139.521 Da / Num. of mol.: 2 / Fragment: UNP residues 372-389 / Source method: obtained synthetically / Details: ACETYLATED P53 LYS-382 / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM Na Hepes pH7.5; 25% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.99→46.56 Å / Num. obs: 38331 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rsym value: 0.047 / Net I/σ(I): 15.43
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3.14 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5913 / Rsym value: 0.506 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3glt

3glt


Resolution: 1.99→46.56 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.913 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 1917 5 %RANDOM
Rwork0.16713 ---
obs0.17005 36411 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å21.21 Å2
2---1.68 Å20 Å2
3---1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.99→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 2 239 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194488
X-RAY DIFFRACTIONr_bond_other_d0.0020.024248
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9686073
X-RAY DIFFRACTIONr_angle_other_deg1.093.0029801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45922.935201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15915733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3511537
X-RAY DIFFRACTIONr_chiral_restr0.1070.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214963
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02934
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4413.8632245
X-RAY DIFFRACTIONr_mcbond_other3.4273.8622244
X-RAY DIFFRACTIONr_mcangle_it4.715.7612794
X-RAY DIFFRACTIONr_mcangle_other4.715.7632795
X-RAY DIFFRACTIONr_scbond_it4.5344.462243
X-RAY DIFFRACTIONr_scbond_other4.5334.4622244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.816.4723280
X-RAY DIFFRACTIONr_long_range_B_refined8.69746.8044828
X-RAY DIFFRACTIONr_long_range_B_other8.68846.7014799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 130 -
Rwork0.272 2460 -
obs--91.52 %

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