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

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Basic information

Entry
Database: PDB / ID: 3rig
TitleSirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase
Components
  • NAD-dependent deacetylase sirtuin-5
  • peptide of histone 3 thioacetyl-lysine 9
KeywordsHYDROLASE / protein lysine demalonylase/desuccinylase / Zn-binding domain / Rossmann fold / Mitochondria
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 / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / response to nutrient levels / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / mitochondrion organization / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / mitochondrial intermembrane space / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / transferase activity / gene expression / 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 / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 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
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: 2 Å
AuthorsZhou, Y.
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 13, 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
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 thioacetyl-lysine 9
D: peptide of histone 3 thioacetyl-lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4828
Polymers61,9374
Non-polymers5454
Water3,171176
1
A: NAD-dependent deacetylase sirtuin-5
C: peptide of histone 3 thioacetyl-lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2414
Polymers30,9682
Non-polymers2732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-3 kcal/mol
Surface area12980 Å2
MethodPISA
2
B: NAD-dependent deacetylase sirtuin-5
D: peptide of histone 3 thioacetyl-lysine 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2414
Polymers30,9682
Non-polymers2732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-3 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.538, 67.876, 156.749
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 thioacetyl-lysine 9


Mass: 1293.517 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This human histone 3 N-terminal was chemically modified on residue lysine 9 with thioacetyl.
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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.26 Å3/Da / Density % sol: 45.48 % / Mosaicity: 0.278 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 20% PEG 8000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 41492 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Χ2: 2.004 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-1.985.30.34620320.85699.7
1.98-2.025.70.28520320.854100
2.02-2.066.10.26620370.877100
2.06-2.16.50.23620540.977100
2.1-2.157.10.21720371.041100
2.15-2.27.40.19620701.09100
2.2-2.257.40.18720481.259100
2.25-2.317.40.16520271.299100
2.31-2.387.30.14920861.434100
2.38-2.467.40.14320181.581100
2.46-2.547.30.1320751.658100
2.54-2.657.30.12320601.902100
2.65-2.777.20.11420832.044100
2.77-2.917.20.10420682.219100
2.91-3.17.10.09620872.405100
3.1-3.3370.08720812.862100
3.33-3.676.90.08220903.369100
3.67-4.26.60.07521173.797100
4.2-5.296.20.07321524.21199.8
5.29-505.30.07122384.51597.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å41.55 Å
Translation2.5 Å41.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B4Y

2b4y


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.784 / SU B: 10.826 / SU ML: 0.148 / SU R Cruickshank DPI: 0.213 / SU Rfree: 0.182 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1950 5 %RANDOM
Rwork0.219 ---
obs0.221 38693 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.64 Å2 / Biso mean: 41.687 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20 Å2
2---0.47 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 28 176 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224270
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9585799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57722.473186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80115678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1971539
X-RAY DIFFRACTIONr_chiral_restr0.1270.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213279
X-RAY DIFFRACTIONr_mcbond_it1.0581.52666
X-RAY DIFFRACTIONr_mcangle_it1.79624293
X-RAY DIFFRACTIONr_scbond_it2.73731604
X-RAY DIFFRACTIONr_scangle_it4.2824.51497
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 147 -
Rwork0.252 2682 -
all-2829 -
obs--99.96 %
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)
13.5055-0.4718-2.57351.05070.30052.860.13540.29460.122-0.0540.0030.0177-0.076-0.2637-0.13830.00820.0063-0.00350.273-0.01660.043410.135-9.315-18.227
23.75730.7791-0.9962.80052.89289.14120.69450.12060.8612-0.5444-0.0294-0.0306-1.674-0.43-0.66510.40520.06390.260.26330.05130.284521.2953.937-28.287
33.6545-1.29830.81614.179-1.42298.1595-0.2762-0.5617-0.0850.10160.6370.2858-0.058-2.3699-0.36090.07160.1405-0.01241.62140.31930.25773.252-7.098-47.571
42.07640.465-0.01740.8775-1.39624.57920.0174-0.0933-0.1259-0.1010.02890.01740.24210.1575-0.04630.02630.0096-0.03550.24320.00510.094326.723-7.125-62.857
51.6776-0.4311.66880.463-1.69078.1244-0.1359-0.4957-0.14090.10410.60510.2247-0.4692-2.2907-0.46930.06710.1154-0.01261.11130.2260.25084.846-4.837-55.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 274
2X-RAY DIFFRACTION2A275 - 302
3X-RAY DIFFRACTION3B36 - 59
4X-RAY DIFFRACTION4B74 - 229
5X-RAY DIFFRACTION5B230 - 302

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