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- PDB-3riy: Sirt5 is an NAD-dependent protein lysine demalonylase and desucci... -

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Basic information

Entry
Database: PDB / ID: 3riy
TitleSirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase
Components
  • NAD-dependent deacetylase sirtuin-5
  • peptide of histone 3 N-succinyl lysine 9
KeywordsHYDROLASE / desuccinylase / demalonylase / posttranslational modification / Zn-binding domain / Rossmann fold domain
Function / homology
Function and homology information


protein demalonylation / regulation of ketone biosynthetic process / protein desuccinylation / peptidyl-lysine demalonylation / protein deglutarylation / protein-glutaryllysine deglutarylase activity / peptidyl-lysine desuccinylation / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein deacetylase activity ...protein demalonylation / regulation of ketone biosynthetic process / protein desuccinylation / peptidyl-lysine demalonylation / protein deglutarylation / protein-glutaryllysine deglutarylase activity / peptidyl-lysine desuccinylation / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein deacetylase activity / negative regulation of cardiac muscle cell apoptotic process / protein deacetylation / epigenetic regulation of gene expression / : / Chromatin modifying enzymes / negative regulation of reactive oxygen species metabolic process / NAD+ binding / NAD+ ADP-ribosyltransferase activity / telomere organization / Interleukin-7 signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / mitochondrion organization / DNA methylation / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / NoRC negatively regulates rRNA expression / Transcriptional regulation by small RNAs / response to nutrient levels / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / mitochondrial intermembrane space / RMTs methylate histone arginines / HDMs demethylate histones / Transcriptional activation of mitochondrial biogenesis / nucleosome assembly / Meiotic recombination / Pre-NOTCH Transcription and Translation / PKMTs methylate histone lysines / HCMV Early Events / structural constituent of chromatin / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / mitochondrial matrix / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / mitochondrion / DNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane / nucleoplasm / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sir2 family / Sirtuin family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sir2 family / Sirtuin family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Histone H3.1 / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsZhou, Y. / Hao, Q.
CitationJournal: Science / Year: 2011
Title: Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase
Authors: Du, J. / Zhou, Y. / Su, X. / Yu, J.J. / Khan, S. / Jiang, H. / Kim, J. / Woo, J. / Kim, J.H. / Choi, B.H. / He, B. / Chen, W. / Zhang, S. / Cerione, R.A. / Auwerx, J. / Hao, Q. / Lin, H.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase sirtuin-5
B: NAD-dependent deacetylase sirtuin-5
C: peptide of histone 3 N-succinyl lysine 9
D: peptide of histone 3 N-succinyl lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4788
Polymers62,0214
Non-polymers1,4584
Water12,430690
1
A: NAD-dependent deacetylase sirtuin-5
D: peptide of histone 3 N-succinyl lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7394
Polymers31,0102
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent deacetylase sirtuin-5
C: peptide of histone 3 N-succinyl lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7394
Polymers31,0102
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.691, 69.417, 156.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD-dependent deacetylase sirtuin-5 / SIR2-like protein 5


Mass: 29674.795 Da / Num. of mol.: 2 / Fragment: UNP residues 34-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L5, SIRT5 / Plasmid: pDEST-F1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 R2
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide peptide of histone 3 N-succinyl lysine 9


Mass: 1335.487 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: histone 3 (residue 4-15) was chemically synthesized.
References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.63 % / Mosaicity: 0.6 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 4000, 6% Glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 83831 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.066 / Χ2: 1.979 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.55-1.585.70.39840881.62498.5
1.58-1.6160.34940941.69598.9
1.61-1.646.40.30340911.73999
1.64-1.676.90.28341461.75599.4
1.67-1.717.10.25541711.78499.9
1.71-1.757.20.21641371.83399.7
1.75-1.797.20.18841131.89199.9
1.79-1.847.20.16341741.93899.7
1.84-1.897.30.1441781.969100
1.89-1.957.30.1241772.035100
1.95-2.027.30.10141622.069100
2.02-2.17.40.08841952.071100
2.1-2.27.40.07841782.076100
2.2-2.327.30.0742072.098100
2.32-2.467.30.06341952.067100
2.46-2.657.30.05642511.962100
2.65-2.927.30.05142351.955100
2.92-3.347.30.04642622.021100
3.34-4.217.20.04243092.15499.9
4.21-506.70.04644682.63998.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å37.05 Å
Translation2.5 Å37.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RIG
Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1867 / WRfactor Rwork: 0.145 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8951 / SU B: 2.511 / SU ML: 0.042 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.0777 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 4177 5 %RANDOM
Rwork0.1437 ---
obs0.1461 83691 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.82 Å2 / Biso mean: 16.6283 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0 Å2
2--1.04 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 90 690 5060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224715
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9776443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22122.488205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93215751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7731544
X-RAY DIFFRACTIONr_chiral_restr0.140.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213660
X-RAY DIFFRACTIONr_mcbond_it2.1831.52884
X-RAY DIFFRACTIONr_mcangle_it3.08824661
X-RAY DIFFRACTIONr_scbond_it4.28531831
X-RAY DIFFRACTIONr_scangle_it6.0314.51759
X-RAY DIFFRACTIONr_rigid_bond_restr2.49734715
X-RAY DIFFRACTIONr_sphericity_free10.5163692
X-RAY DIFFRACTIONr_sphericity_bonded5.85934569
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 290 -
Rwork0.181 5669 -
all-5959 -
obs--97.69 %

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