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- PDB-8gbn: Structure of Apo Human SIRT5 P114T Mutant -

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Basic information

Entry
Database: PDB / ID: 8gbn
TitleStructure of Apo Human SIRT5 P114T Mutant
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: 2.7 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

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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)59,3486
Polymers59,0942
Non-polymers2554
Water1,65792
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6743
Polymers29,5471
Non-polymers1272
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)29,6743
Polymers29,5471
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.017, 114.896, 56.265
Angle α, β, γ (deg.)90.00, 90.14, 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: 29546.756 Da / Num. of mol.: 2 / Mutation: P114T
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 20% PEG 10K, 10 mM Praseodymium (III) acetate hydrate

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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: 2.7→41.02 Å / Num. obs: 13273 / % possible obs: 92.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.612 / Num. unique obs: 1062

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Processing

Software
NameClassification
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.02 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.337
RfactorNum. reflection% reflectionSelection details
Rfree0.231 616 4.63 %RANDOM
Rwork0.182 ---
obs0.184 13302 92.3 %-
Displacement parametersBiso mean: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.8451 Å20 Å2-0.2899 Å2
2---2.3149 Å20 Å2
3---1.4698 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.7→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 10 92 3904
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013910HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1723SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes670HARMONIC5
X-RAY DIFFRACTIONt_it3910HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion2.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
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_contact4410SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.74 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.1934 -2.03 %
Rwork0.2237 435 -
all0.223 444 -
obs--68.39 %

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