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- PDB-4zzj: SIRT1/Activator/Substrate Complex -

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Basic information

Entry
Database: PDB / ID: 4zzj
TitleSIRT1/Activator/Substrate Complex
Components
  • Ac-p53
  • NAD-dependent protein deacetylase sirtuin-1
KeywordsHYDROLASE / Sirtuin / Activator / Deacylase / Complex
Function / homology
Function and homology information


pyrimidine dimer repair by nucleotide-excision repair / negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / histone decrotonylase activity, NAD-dependent / negative regulation of protein acetylation / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / regulation of endodeoxyribonuclease activity ...pyrimidine dimer repair by nucleotide-excision repair / negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / histone decrotonylase activity, NAD-dependent / negative regulation of protein acetylation / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / regulation of endodeoxyribonuclease activity / positive regulation of cAMP-dependent protein kinase activity / negative regulation of peptidyl-lysine acetylation / peptidyl-lysine acetylation / histone H3K14 deacetylase activity, NAD-dependent / regulation of peroxisome proliferator activated receptor signaling pathway / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / positive regulation of macrophage apoptotic process / histone H4K12 deacetylase activity, hydrolytic mechanism / negative regulation of triglyceride biosynthetic process / triglyceride mobilization / keratin filament binding / NAD-dependent protein lysine delactylase activity / histone H3K9 deacetylase activity, NAD-dependent / positive regulation of smooth muscle cell differentiation / regulation of brown fat cell differentiation / Regulation of MITF-M dependent genes involved in metabolism / leptin-mediated signaling pathway / regulation of lipid storage / bHLH transcription factor binding / positive regulation of macrophage cytokine production / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / intracellular triglyceride homeostasis / HLH domain binding / negative regulation of phosphorylation / response to leptin / regulation of transcription by glucose / deacetylase activity / regulation of bile acid biosynthetic process / negative regulation of androgen receptor signaling pathway / positive regulation of adaptive immune response / rDNA heterochromatin / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / histone deacetylase activity, NAD-dependent / positive regulation of MHC class II biosynthetic process / rDNA heterochromatin formation / protein deacetylation / negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / chromatin silencing complex / single strand break repair / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / negative regulation of TOR signaling / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / muscle organ development / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / Regulation of FOXO transcriptional activity by acetylation / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / histone deacetylase activity / DNA methylation-dependent constitutive heterochromatin formation / positive regulation of programmed necrotic cell death / mitogen-activated protein kinase binding / RUNX3 regulates CDKN1A transcription / negative regulation of cellular senescence / protein lysine deacetylase activity / stress-induced premature senescence / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / nuclear inner membrane / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / negative regulation of fat cell differentiation / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / regulation of centrosome duplication / white fat cell differentiation / UV-damage excision repair / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of cell cycle / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / DNA synthesis involved in DNA repair / energy homeostasis / Zygotic genome activation (ZGA)
Similarity search - Function
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 ...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
Chem-4TQ / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cellular tumor antigen p53 / NAD-dependent protein deacetylase sirtuin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7403 Å
AuthorsDai, H.
CitationJournal: Nat Commun / Year: 2015
Title: Crystallographic structure of a small molecule SIRT1 activator-enzyme complex.
Authors: Dai, H. / Case, A.W. / Riera, T.V. / Considine, T. / Lee, J.E. / Hamuro, Y. / Zhao, H. / Jiang, Y. / Sweitzer, S.M. / Pietrak, B. / Schwartz, B. / Blum, C.A. / Disch, J.S. / Caldwell, R. / ...Authors: Dai, H. / Case, A.W. / Riera, T.V. / Considine, T. / Lee, J.E. / Hamuro, Y. / Zhao, H. / Jiang, Y. / Sweitzer, S.M. / Pietrak, B. / Schwartz, B. / Blum, C.A. / Disch, J.S. / Caldwell, R. / Szczepankiewicz, B. / Oalmann, C. / Yee Ng, P. / White, B.H. / Casaubon, R. / Narayan, R. / Koppetsch, K. / Bourbonais, F. / Wu, B. / Wang, J. / Qian, D. / Jiang, F. / Mao, C. / Wang, M. / Hu, E. / Wu, J.C. / Perni, R.B. / Vlasuk, G.P. / Ellis, J.L.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 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 sirtuin-1
B: Ac-p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5177
Polymers41,1112
Non-polymers1,4065
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area18180 Å2
MethodPISA
2
A: NAD-dependent protein deacetylase sirtuin-1
B: Ac-p53
hetero molecules

A: NAD-dependent protein deacetylase sirtuin-1
B: Ac-p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,03414
Polymers82,2234
Non-polymers2,81110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area6360 Å2
ΔGint-22 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.510, 94.510, 356.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NAD-dependent protein deacetylase sirtuin-1 / hSIRT1 / Regulatory protein SIR2 homolog 1 / SIR2-like protein 1 / hSIR2


Mass: 40125.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT1, SIR2L1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Ac-p53


Mass: 986.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637*PLUS

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Non-polymers , 5 types, 49 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#5: Chemical ChemComp-4TQ / (3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide


Mass: 493.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22F3N5O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 5% v/v Tacsimate, pH .00.1 M HEPES pH 7.0 and 10% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.74→91.36 Å / Num. obs: 21821 / % possible obs: 99.5 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.7
Reflection shellResolution: 2.74→2.86 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLU and 4IG9

3glu

4ig9


Resolution: 2.7403→45.68 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1116 5.13 %
Rwork0.1825 --
obs0.1844 21765 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7403→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 93 44 2949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052998
X-RAY DIFFRACTIONf_angle_d0.9384075
X-RAY DIFFRACTIONf_dihedral_angle_d14.451138
X-RAY DIFFRACTIONf_chiral_restr0.036444
X-RAY DIFFRACTIONf_plane_restr0.006523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7403-2.8650.33171240.27252541X-RAY DIFFRACTION99
2.865-3.0160.34821370.26672504X-RAY DIFFRACTION99
3.016-3.20490.29121490.24762513X-RAY DIFFRACTION99
3.2049-3.45230.25321470.21792535X-RAY DIFFRACTION99
3.4523-3.79960.21191360.18452583X-RAY DIFFRACTION100
3.7996-4.3490.20391510.14512564X-RAY DIFFRACTION100
4.349-5.47780.16691330.14452629X-RAY DIFFRACTION100
5.4778-45.68630.20851390.18042780X-RAY DIFFRACTION99
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)
10.32980.2448-0.15930.95420.31960.572-0.20360.23320.0131-0.2010.30090.0657-0.0108-0.0239-00.5961-0.0657-0.02280.54720.03420.54642.528554.669110.5441
20.10780.18390.17340.77570.01650.4547-0.03660.0353-0.02890.26090.09640.0097-0.1040.020500.4627-0.02340.01740.35370.03980.4487.081764.734830.5229
30.16320.030.11020.0643-0.02180.1638-0.00460.23780.0198-0.07080.2697-0.2363-0.3520.07570.00240.6476-0.1508-0.00710.58280.04380.531616.716776.462310.8415
40.0121-0.0012-0.00540.01130.00620.0040.17530.0226-0.0786-0.14290.18760.14990.26510.04310.00010.5724-0.1533-0.0690.5595-0.02520.83170.132254.136225.1641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 183 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 481 )
3X-RAY DIFFRACTION3chain 'A' and (resid 482 through 660 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )

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