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- PDB-4bv2: CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2... -

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Entry
Database: PDB / ID: 4bv2
TitleCRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE
Components
  • CELLULAR TUMOR ANTIGEN P53
  • NAD-DEPENDENT PROTEIN DEACETYLASE
KeywordsHYDROLASE / NAD-DEPENDENT DEACETYLASE / SIRTUIN / INHIBITOR COMPLEX / EX-527 / ACETYLATED ADP-RIBOSE / HYDROLASE-HYDROLASE
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 / 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 ...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 / 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 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / bone marrow development / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / 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 / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / negative regulation of mitophagy / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / 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 by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / general transcription initiation factor binding / cellular response to actinomycin D / NAD+ binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of execution phase of apoptosis / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / viral process / Pyroptosis / hematopoietic stem cell differentiation / response to X-ray / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / negative regulation of proteolysis / MDM2/MDM4 family protein binding
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 / TPP-binding domain / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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
2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE / Chem-OCZ / Cellular tumor antigen p53 / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGertz, M. / Weyand, M. / Steegborn, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism
Authors: Gertz, M. / Fischer, F. / Nguyen, G.T.T. / Lakshminarasimhan, M. / Schutkowski, M. / Weyand, M. / Steegborn, C.
History
DepositionJun 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.pdbx_dist_value / _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
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: NAD-DEPENDENT PROTEIN DEACETYLASE
B: NAD-DEPENDENT PROTEIN DEACETYLASE
E: CELLULAR TUMOR ANTIGEN P53
H: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,16610
Polymers58,3354
Non-polymers1,8316
Water00
1
A: NAD-DEPENDENT PROTEIN DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4854
Polymers27,5701
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-DEPENDENT PROTEIN DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4854
Polymers27,5701
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: CELLULAR TUMOR ANTIGEN P53


  • defined by author
  • 1.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5981
Polymers1,5981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: CELLULAR TUMOR ANTIGEN P53


  • defined by author
  • 1.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5981
Polymers1,5981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: NAD-DEPENDENT PROTEIN DEACETYLASE
H: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0835
Polymers29,1682
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4.7 kcal/mol
Surface area11410 Å2
MethodPISA
6
A: NAD-DEPENDENT PROTEIN DEACETYLASE
E: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0835
Polymers29,1682
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-3.9 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.950, 45.950, 241.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A2 - 245
2113B2 - 245

NCS oper:
IDCodeMatrixVector
1given(-0.999, -0.0332, 0.031), (-0.006934, 0.7859, 0.6183), (-0.0449, 0.6174, -0.7853)122.6, 27.25, -76.24
2given(1), (1), (1)
3given(-0.998967, -0.006905, -0.04492), (-0.033196, 0.785921, 0.617436), (0.03104, 0.618289, -0.785338)119.2344, 29.72567, -80.52349

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Components

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE / REGULATORY PROTEIN SIR2 HOMOLOG / SIR2TM / NAD-DEPENDENT PROTEIN DEACETYLASE SIR2


Mass: 27569.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide CELLULAR TUMOR ANTIGEN P53 / DEACETYLATED P53-PEPTIDE / ANTIGEN NY-CO-13 / PHOSPHOPROTEIN P53 / TUMOR SUPPRESSOR P53 / P53


Mass: 1597.900 Da / Num. of mol.: 2 / Fragment: RESIDUES 380-384 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P04637
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OCZ / (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide


Mass: 248.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13ClN2O
#5: Chemical ChemComp-OAD / 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE


Type: RNA linking / Mass: 601.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N5O15P2
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: 2.26 Å3/Da / Density % sol: 45.61 % / Description: NONE
Crystal growpH: 5.9 / Details: 20% PEG 6000, 0.1 M BIS-TRIS PH5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.3→60.47 Å / Num. obs: 31261 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.54
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YC5

1yc5


Resolution: 3.3→60.47 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.845 / SU B: 108.33 / SU ML: 0.846 / Cross valid method: THROUGHOUT / ESU R Free: 0.787 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.31781 374 5 %RANDOM
Rwork0.2452 ---
obs0.2489 7099 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.439 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→60.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 114 0 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1332.0255331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9195468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44724.398166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.50215696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2741522
X-RAY DIFFRACTIONr_chiral_restr0.1350.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212860
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.0966.0581893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.6249.0772354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0816.2662044
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A883loose positional0.065
2B883loose positional0.065
1A916tight thermal6.690.5
2B916tight thermal6.690.5
1A883loose thermal8.7410
2B883loose thermal8.7410
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 26 -
Rwork0.307 500 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.01063.3286-0.05487.05231.01913.379-0.4827-0.7262-0.05990.69520.2604-0.25430.29130.25740.22230.4540.3159-0.02080.26440.0570.31849.432363.8727-6.4175
26.4119-2.82220.11584.25770.72934.0026-0.05421.20760.4468-0.162-0.3182-0.0634-0.2523-0.11240.37230.4023-0.2396-0.10.42040.02540.338870.916372.8163-34.1303
3207.483470.9652-182.56237.7495-89.4486214.75455.2158-3.50211.1176-0.3202-2.98831.0105-0.38626.6769-2.22750.7343-0.0482-0.23830.6239-0.14740.451271.014779.3658-31.9064
47.703214.180745.485112.445331.5925300.15780.9175-0.9369-0.1188-2.6385-1.1743-2.34578.2178-5.87670.25690.6210.2423-0.20360.8328-0.00951.082849.300870.1896-4.3862
55.00554.59883.173726.63863.76782.059-2.7171-0.21010.557-3.55042.31410.1554-1.67720.0180.4032.06070.33780.07920.50670.17050.317941.474967.687-5.7857
60.89733.68711.309315.97955.73862.07910.07170.1664-0.01560.85870.2972-0.69350.34270.0629-0.3690.3929-0.0039-0.32840.82210.51430.788778.458476.6872-31.5204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 245
2X-RAY DIFFRACTION2B3 - 246
3X-RAY DIFFRACTION3A1247
4X-RAY DIFFRACTION4B1247
5X-RAY DIFFRACTION5A1248
6X-RAY DIFFRACTION6B1248

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