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Yorodumi- PDB-3riy: Sirt5 is an NAD-dependent protein lysine demalonylase and desucci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3riy | ||||||
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Title | Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase | ||||||
Components |
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Keywords | HYDROLASE / desuccinylase / demalonylase / posttranslational modification / Zn-binding domain / Rossmann fold domain | ||||||
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 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 deacetylase activity / protein deacetylation / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Chromatin modifying enzymes / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrion organization / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / response to nutrient levels / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / mitochondrial intermembrane space / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / transferase activity / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / mitochondrial matrix / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / mitochondrion / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Zhou, Y. / Hao, Q. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3riy.cif.gz | 267.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3riy.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 3riy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/3riy ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3riy | HTTPS FTP |
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-Related structure data
Related structure data | 3rigSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % / Mosaicity: 0.6 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 16% PEG 4000, 6% Glycerol, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.82 Å2 / Biso mean: 16.6283 Å2 / Biso min: 3.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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