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- PDB-8gbl: Structure of Apo Human SIRT5 -

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Basic information

Entry
Database: PDB / ID: 8gbl
TitleStructure of Apo Human SIRT5
ComponentsNAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsTRANSFERASE / Deacetylase
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / NAD-dependent histone deacetylase activity / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPetrunak, E.M. / Stuckey, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Iscience / Year: 2024
Title: Human SIRT5 variants with reduced stability and activity do not cause neuropathology in mice.
Authors: Yuan, T. / Kumar, S. / Skinner, M.E. / Victor-Joseph, R. / Abuaita, M. / Keijer, J. / Zhang, J. / Kunkel, T.J. / Liu, Y. / Petrunak, E.M. / Saunders, T.L. / Lieberman, A.P. / Stuckey, J.A. / ...Authors: Yuan, T. / Kumar, S. / Skinner, M.E. / Victor-Joseph, R. / Abuaita, M. / Keijer, J. / Zhang, J. / Kunkel, T.J. / Liu, Y. / Petrunak, E.M. / Saunders, T.L. / Lieberman, A.P. / Stuckey, J.A. / Neamati, N. / Al-Murshedi, F. / Alfadhel, M. / Spelbrink, J.N. / Rodenburg, R. / de Boer, V.C.J. / Lombard, D.B.
History
DepositionFeb 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2164
Polymers59,0862
Non-polymers1312
Water2,090116
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6082
Polymers29,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6082
Polymers29,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.624, 112.528, 56.083
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 29542.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXA8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES 6.5, 25% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.25→41.62 Å / Num. obs: 23939 / % possible obs: 96.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.756 / Num. unique obs: 1890

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Processing

Software
NameClassification
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→41.62 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.318 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1143 4.77 %RANDOM
Rwork0.215 ---
obs0.217 23941 96.7 %-
Displacement parametersBiso mean: 37.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.7803 Å2
2--1.7168 Å20 Å2
3----1.3269 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.24→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 2 116 3909
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1256SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes665HARMONIC5
X-RAY DIFFRACTIONt_it3886HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion16.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4401SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.27 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3204 -2.92 %
Rwork0.2163 465 -
all0.2194 479 -
obs--64.45 %
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)
1-0.0006-0.69950.58425.083-0.73454.3571-0.00360.6702-0.3909-0.68130.36630.53570.2202-0.4142-0.3627-0.1088-0.0838-0.03090.07890.081-0.25980.8950.743-1.017
24.05340.85791.41095.4676-0.75525.6918-0.22520.663-0.6121-0.52530.3565-0.6666-0.16560.6118-0.1313-0.0714-0.11880.1345-0.0161-0.12110.053423.0230.44520.579
31.9030.16151.07481.7035-0.18123.43970.008-0.06950.0044-0.0790.1038-0.08-0.3964-0.2259-0.1119-0.04640.01960.0652-0.0681-0.001-0.09159.9283.50820.666
49.15533.2338-1.96785.4097-4.94615.1399-0.0209-0.0283-0.5694-0.53750.18540.67810.7393-0.2284-0.1645-0.02950.01160.0272-0.0294-0.0604-0.05541.446-8.88.335
51.08540.4066-0.68278.25172.14589.66210.04510.26-0.2523-0.36180.1278-0.24540.6928-0.5516-0.173-0.0013-0.0133-0.03190.04420.0648-0.22984.025-2.494-3.891
60.0010.6581-0.9916.70740.98247.4742-0.13320.70970.3063-0.62390.27210.0188-0.2622-0.3872-0.13880.003-0.0753-0.0990.0161-0.0431-0.204415.874-29.7358.395
72.88610.6854-2.12362.139-0.06825.1538-0.16630.20550.0621-0.20510.09430.18080.474-0.31740.072-0.1404-0.0385-0.1303-0.16-0.0197-0.13748.578-32.84425.688
84.55362.4022-2.1775.60880.02092.04420.04030.04040.4578-0.11460.2060.64530.3863-0.5498-0.2463-0.1436-0.0149-0.04860.0511-0.025-0.00561.858-29.67337.823
93.06032.61281.29197.64934.9726.6769-0.01760.14640.3146-0.37850.1198-0.5122-0.77070.3512-0.1022-0.0391-0.0157-0.0638-0.07880.0161-0.024621.011-21.14917.435
100.73750.467-0.4849.01380.85567.17440.0130.54560.3571-0.70030.01410.2952-0.9775-0.0463-0.02710.1276-0.0465-0.0583-0.09670.0015-0.228716.683-25.3435.061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|38 - A|67 }A38 - 67
2X-RAY DIFFRACTION2{ A|68 - A|112 }A68 - 112
3X-RAY DIFFRACTION3{ A|113 - A|227 }A113 - 227
4X-RAY DIFFRACTION4{ A|228 - A|262 }A228 - 262
5X-RAY DIFFRACTION5{ A|263 - A|302 }A263 - 302
6X-RAY DIFFRACTION6{ B|38 - B|75 }B38 - 75
7X-RAY DIFFRACTION7{ B|76 - B|190 }B76 - 190
8X-RAY DIFFRACTION8{ B|191 - B|225 }B191 - 225
9X-RAY DIFFRACTION9{ B|226 - B|252 }B226 - 252
10X-RAY DIFFRACTION10{ B|257 - B|302 }B257 - 302

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