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- PDB-8z57: Crystal structure of human Q140L-SIRT5 in complex with succinylat... -

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Basic information

Entry
Database: PDB / ID: 8z57
TitleCrystal structure of human Q140L-SIRT5 in complex with succinylated Prx1 fragment and ADP ribose
Components
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
  • Peroxiredoxin-1 fragment
KeywordsTRANSFERASE / SIRT5 / succinyl lysine / deacylase
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 / leukocyte activation / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / leukocyte activation / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / NAD-dependent protein lysine deacetylase activity / thioredoxin peroxidase activity / histone deacetylase activity, NAD-dependent / protein deacetylation / natural killer cell activation / negative regulation of cardiac muscle cell apoptotic process / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / natural killer cell mediated cytotoxicity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / negative regulation of reactive oxygen species metabolic process / NAD+ binding / canonical NF-kappaB signal transduction / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / removal of superoxide radicals / cell redox homeostasis / skeletal system development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / mitochondrion organization / peroxidase activity / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / melanosome / fibroblast proliferation / response to oxidative stress / cell population proliferation / mitochondrial matrix / cadherin binding / mitochondrion / extracellular space / RNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class III / Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Sirtuin, catalytic core small domain superfamily / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Sirtuin family / : ...Sirtuin, class III / Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Sirtuin, catalytic core small domain superfamily / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Peroxiredoxin-1 / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYokoyama, T. / Takayama, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2024
Title: SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD + -binding pocket.
Authors: Yokoyama, T. / Takayama, Y. / Mizuguchi, M. / Nabeshima, Y. / Kusaka, K.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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: Peroxiredoxin-1 fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7384
Polymers31,2462
Non-polymers4932
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.084, 73.043, 162.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-582-

HOH

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Components

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


Mass: 29999.221 Da / Num. of mol.: 1 / Mutation: Q140L
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: Protein/peptide Peroxiredoxin-1 fragment / Prx1 fragment


Mass: 1246.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q06830
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 3350, 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.96→40.61 Å / Num. obs: 20158 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rrim(I) all: 0.082 / Net I/σ(I): 15.5
Reflection shellResolution: 1.96→2.01 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1361 / CC1/2: 0.805 / Rrim(I) all: 1.051

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→36.522 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 1024 5.1 %
Rwork0.1987 --
obs0.2013 20091 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→36.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 35 99 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062158
X-RAY DIFFRACTIONf_angle_d0.8052931
X-RAY DIFFRACTIONf_dihedral_angle_d23.284804
X-RAY DIFFRACTIONf_chiral_restr0.072318
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.06330.3171640.28572656X-RAY DIFFRACTION100
2.0633-2.19260.30671550.24292654X-RAY DIFFRACTION100
2.1926-2.36190.28341390.21932682X-RAY DIFFRACTION100
2.3619-2.59950.25291300.20852737X-RAY DIFFRACTION100
2.5995-2.97550.24521440.21092706X-RAY DIFFRACTION100
2.9755-3.74820.25951470.1982762X-RAY DIFFRACTION100
3.7482-36.5220.2291450.17562870X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 27.0838 Å / Origin y: 1.3331 Å / Origin z: 62.1588 Å
111213212223313233
T0.4308 Å20.0021 Å20.0026 Å2-0.3446 Å2-0.0274 Å2--0.3134 Å2
L0.6267 °20.3577 °20.1281 °2-3.2628 °2-1.1098 °2--4.0544 °2
S-0.0933 Å °0.0384 Å °-0.0272 Å °-0.3153 Å °0.1697 Å °-0.1528 Å °0.1143 Å °0.1284 Å °-0.0683 Å °
Refinement TLS groupSelection details: not resname HOH and not resname ANP and not resname MG

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