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- PDB-4zzh: SIRT1/Activator Complex -

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Basic information

Entry
Database: PDB / ID: 4zzh
TitleSIRT1/Activator Complex
ComponentsNAD-dependent protein deacetylase sirtuin-1
KeywordsHydrolase/hydrolase activator / Sirtuin / Activator / Deacylase / Complex / Hydrolase-hydrolase activator complex
Function / homology
Function and homology information


negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / negative regulation of peptidyl-lysine acetylation / eNoSc complex / regulation of peroxisome proliferator activated receptor signaling pathway ...negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / negative regulation of peptidyl-lysine acetylation / eNoSc complex / regulation of peroxisome proliferator activated receptor signaling pathway / regulation of transcription by glucose / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / positive regulation of macrophage apoptotic process / positive regulation of cAMP-dependent protein kinase activity / negative regulation of triglyceride biosynthetic process / regulation of endodeoxyribonuclease activity / behavioral response to starvation / pyrimidine dimer repair by nucleotide-excision repair / triglyceride mobilization / peptidyl-lysine acetylation / keratin filament binding / NAD-dependent protein lysine delactylase activity / leptin-mediated signaling pathway / Regulation of MITF-M dependent genes involved in metabolism / HLH domain binding / regulation of lipid storage / regulation of brown fat cell differentiation / bHLH transcription factor binding / deacetylase activity / positive regulation of smooth muscle cell differentiation / negative regulation of protein acetylation / response to leptin / intracellular triglyceride homeostasis / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of phosphorylation / positive regulation of adaptive immune response / negative regulation of androgen receptor signaling pathway / rDNA heterochromatin / ovulation from ovarian follicle / regulation of centrosome duplication / regulation of bile acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / negative regulation of signal transduction by p53 class mediator / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / single strand break repair / rDNA heterochromatin formation / histone deacetylase activity, NAD-dependent / histone H4K12 deacetylase activity, hydrolytic mechanism / protein deacetylation / positive regulation of MHC class II biosynthetic process / chromatin silencing complex / UV-damage excision repair / negative regulation of TOR signaling / nuclear inner membrane / Regulation of FOXO transcriptional activity by acetylation / mitogen-activated protein kinase binding / protein lysine deacetylase activity / positive regulation of macrophage cytokine production / stress-induced premature senescence / muscle organ development / positive regulation of double-strand break repair / histone deacetylase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA synthesis involved in DNA repair / negative regulation of fat cell differentiation / DNA repair-dependent chromatin remodeling / negative regulation of NF-kappaB transcription factor activity / intracellular glucose homeostasis / negative regulation of DNA damage response, signal transduction by p53 class mediator / macrophage differentiation / white fat cell differentiation / positive regulation of macroautophagy / negative regulation of cell cycle / regulation of glucose metabolic process / negative regulation of cellular senescence / NAD+ binding / positive regulation of cholesterol efflux / positive regulation of blood vessel endothelial cell migration / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Regulation of HSF1-mediated heat shock response / negative regulation of hippo signaling / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / heterochromatin / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to glucose starvation / regulation of cellular response to heat / energy homeostasis / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / positive regulation of endothelial cell proliferation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...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. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4TO / NAD-dependent protein deacetylase sirtuin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1001 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 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6823
Polymers40,1251
Non-polymers5572
Water00
1
A: NAD-dependent protein deacetylase sirtuin-1
hetero molecules

A: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3646
Polymers80,2512
Non-polymers1,1144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area3430 Å2
ΔGint-16 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.190, 111.640, 132.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4TO / (4S)-N-[3-(1,3-oxazol-5-yl)phenyl]-7-[3-(trifluoromethyl)phenyl]-3,4-dihydro-1,4-methanopyrido[2,3-b][1,4]diazepine-5(2H)-carboxamide


Mass: 491.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H20F3N5O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride, 0.1 M Tris pH 8.5, and 16 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3.1→45.67 Å / Num. obs: 13615 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.4
Reflection shellResolution: 3.1→3.34 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
xia2data scaling
xia2data reduction
RefinementResolution: 3.1001→45.666 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 675 4.96 %
Rwork0.1865 --
obs0.1889 13610 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1001→45.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 37 0 2750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062829
X-RAY DIFFRACTIONf_angle_d1.0393846
X-RAY DIFFRACTIONf_dihedral_angle_d14.1291076
X-RAY DIFFRACTIONf_chiral_restr0.039422
X-RAY DIFFRACTIONf_plane_restr0.005500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.33930.37741300.29742547X-RAY DIFFRACTION99
3.3393-3.67530.30881330.24242554X-RAY DIFFRACTION99
3.6753-4.20680.21031320.18172559X-RAY DIFFRACTION100
4.2068-5.29880.21221350.16212605X-RAY DIFFRACTION99
5.2988-45.67130.2231450.16562670X-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)
11.4090.26430.65332.0066-0.24113.15360.1336-0.1466-0.11330.0543-0.0274-0.09690.4614-0.2412-0.10580.6020.0066-0.04250.688-0.02960.722518.4992-47.4175-6.056
23.013-0.1684-0.28643.3911-0.76911.9895-0.0905-0.4151.1083-0.04-0.0619-0.4258-0.771-0.07350.15891.09520.0801-0.17560.8452-0.12771.106918.4042-17.7405-22.8322
33.7232-0.127-0.26834.72550.36272.9026-0.0876-0.2331-0.046-0.8021-0.0386-0.1048-0.1703-0.04330.1380.76760.0338-0.04240.723-0.02590.621418.2033-43.3574-25.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 183 through 278 )
2X-RAY DIFFRACTION2chain 'A' and (resid 279 through 439 )
3X-RAY DIFFRACTION3chain 'A' and (resid 440 through 658 )

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