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Basic information

Entry
Database: PDB / ID: 4f4u
TitleThe bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5
Components
  • NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
  • peptide from Histone H3.1
KeywordsHYDROLASE / Zn-binding domain / Rossmann fold domain / NAD-dependent demalonylase and desuccinylase / mitochondrial sirtuin
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 / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates 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 / NoRC negatively regulates rRNA expression / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / B-WICH complex positively regulates rRNA expression / 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 / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / 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
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 ...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 / Resolution: 2 Å
AuthorsZhou, Y. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)
Authors: Zhou, Y. / Zhang, H. / He, B. / Du, J. / Lin, H. / Cerione, R.A. / Hao, Q.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 15, 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
Revision 1.3Nov 8, 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 lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
B: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
C: peptide from Histone H3.1
D: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1516
Polymers62,0214
Non-polymers1312
Water4,288238
1
A: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
C: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0763
Polymers31,0102
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
D: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0763
Polymers31,0102
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.687, 67.025, 157.627
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 lysine demalonylase and desuccinylase sirtuin-5, mitochondrial / SIR2-like protein 5


Mass: 29674.795 Da / Num. of mol.: 2 / Fragment: UNP Residue 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 from Histone H3.1 / / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1335.487 Da / Num. of mol.: 2 / Fragment: UNP residue 5-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.24 Å3/Da / Density % sol: 45.18 % / Mosaicity: 0.99 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 11, 2009
RadiationMonochromator: Horizontal bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 39242 / Num. obs: 38953 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Χ2: 2.448 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.036.10.48818990.812197.4
2.03-2.076.50.42618610.876199.3
2.07-2.116.80.38319500.944199.8
2.11-2.1570.35219051.0511100
2.15-2.27.10.32519481.1761100
2.2-2.257.20.29119111.361100
2.25-2.317.20.26319411.4231100
2.31-2.377.20.22619221.6781100
2.37-2.447.20.2219251.8571100
2.44-2.527.20.19619612.0671100
2.52-2.617.10.17919212.271100
2.61-2.717.10.1619282.582199.9
2.71-2.8470.14119552.871100
2.84-2.9970.13119433.3831100
2.99-3.176.90.11219623.69199.9
3.17-3.426.70.09519654.103199.9
3.42-3.766.30.0819774.301199.2
3.76-4.3160.07219674.323199.1
4.31-5.436.20.06920134.264199.6
5.43-5060.06620994.418197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
PHENIXdev_1051refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RIY

3riy


Resolution: 2→28.55 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1927 5.01 %random
Rwork0.218 ---
all0.2245 39242 --
obs0.2202 38428 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 58.3339 Å2 / Biso min: 28.56 Å2
Refinement stepCycle: LAST / Resolution: 2→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 2 238 4394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074286
X-RAY DIFFRACTIONf_angle_d0.9955804
X-RAY DIFFRACTIONf_chiral_restr0.064630
X-RAY DIFFRACTIONf_plane_restr0.005766
X-RAY DIFFRACTIONf_dihedral_angle_d13.2261576
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)
13.3357-1.1721.01123.4534-0.65062.5839-0.2588-0.65110.12220.30650.27920.3708-0.7415-1.2498-0.00910.60660.28980.00161.08530.1090.3739-21.1156-4.184429.7185
23.94341.31433.51557.3916-1.15527.666-0.3054-0.13480.359-0.31760.06020.3594-0.2582-0.44210.33480.37910.0729-0.03040.26590.00570.2873.1051.129710.5372
32.26091.7686-0.91023.606-1.62617.5581-0.2183-0.3727-0.13140.05990.2079-0.08630.7326-0.31050.09560.53430.1490.02720.51230.08410.3112-9.6898-12.585428.5859
44.80591.737-0.84191.4905-1.07672.3781-0.48990.0541-0.5985-0.55160.1916-0.20940.7557-0.04580.28510.63020.05160.0520.3020.03170.32761.6875-10.358510.5575
50.806-0.1859-0.12560.64960.76524.1102-0.3328-0.25470.42290.03660.61530.4441-1.1149-1.5876-0.23630.70990.274-0.10161.02470.15920.5387-21.4909-1.777223.7537
61.42761.589-0.64374.30590.6273.22350.22870.1050.6891-0.67920.2014-0.5665-1.14070.4033-0.35320.7288-0.11490.18550.43090.00330.49540.5055-0.782449.0103
78.0672-2.30671.7432.73570.78528.1993-0.31560.78660.60240.07880.3007-0.0335-0.78420.16350.07240.4809-0.12250.13570.3719-0.00250.4444-28.672-4.084867.8021
83.7023-1.2006-1.13585.82610.79636.45120.31110.653-0.1427-0.6806-0.4180.10010.0842-1.1170.07090.40890.0266-0.00260.4547-0.05350.2511-11.1992-12.650750.0499
95.2933-0.6561-0.50122.4083-0.03142.4506-0.1660.6834-0.9150.36980.11960.3763-0.0224-0.06530.02790.39-0.13130.14210.4333-0.1360.5115-28.5688-14.377868.2624
102.77810.3906-1.65595.20851.72985.35780.39810.03660.3682-0.4246-0.1169-0.4722-1.19770.2-0.2710.506-0.07190.0820.3164-0.02610.3847-2.8976-1.982956.5399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 33:68)A33 - 68
2X-RAY DIFFRACTION2(chain A and resid 69:109)A69 - 109
3X-RAY DIFFRACTION3(chain A and resid 110:156)A110 - 156
4X-RAY DIFFRACTION4(chain A and resid 157:242)A157 - 242
5X-RAY DIFFRACTION5(chain A and resid 243:302)A243 - 302
6X-RAY DIFFRACTION6(chain B and resid 32:63)B32 - 63
7X-RAY DIFFRACTION7(chain B and resid 75:108)B75 - 108
8X-RAY DIFFRACTION8(chain B and resid 109:157)B109 - 157
9X-RAY DIFFRACTION9(chain B and resid 158:227)B158 - 227
10X-RAY DIFFRACTION10(chain B and resid 228:302)B228 - 302

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