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- PDB-6ace: histone lysine desuccinylase Sirt5 in complex with succinyl pepti... -

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Basic information

Entry
Database: PDB / ID: 6ace
Titlehistone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
Components
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
  • succinyl peptide H3K122
KeywordsHYDROLASE / histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
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 / histone deacetylase activity, NAD-dependent / negative regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / response to ischemia / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / mitochondrion organization / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / response to nutrient levels / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional activation of mitochondrial biogenesis / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / mitochondrial intermembrane space / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / mitochondrial inner membrane / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / 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 domain / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.2 / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHang, T.R. / Chen, W.B.
Funding support China, 8items
OrganizationGrant numberCountry
2017YFA0503600 China
2016YFA0400903 China
XDB19000000 China
31621002 China
U1532109 China
31700671 China
2017FXCX004 China
1608085QC52 China
CitationJournal: To Be Published
Title: complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122
Authors: Hang, T.R. / Chen, W.B. / Zang, J.Y. / Zhang, X.
History
DepositionJul 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
B: succinyl peptide H3K122
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3495
Polymers30,0992
Non-polymers2503
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.227, 41.169, 55.854
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / histone lysine desuccinylase Sirt5


Mass: 29054.121 Da / Num. of mol.: 1 / Fragment: UNP residues 36-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide succinyl peptide H3K122


Mass: 1045.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M sodium cacodylate (pH 5.5), 25%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.98→61.41 Å / Num. obs: 18297 / % possible obs: 92.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 11
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.516 / Num. unique obs: 674

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIY

3riy


Resolution: 1.98→61.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.122 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26634 862 5.2 %RANDOM
Rwork0.20269 ---
obs0.20609 15569 82.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.09 Å2
2---0.08 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.98→61.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 13 121 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192187
X-RAY DIFFRACTIONr_bond_other_d0.0030.022078
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9632957
X-RAY DIFFRACTIONr_angle_other_deg1.0683.0024779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8035273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5922.79693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15615340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8121518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5852.8671103
X-RAY DIFFRACTIONr_mcbond_other2.5852.8651102
X-RAY DIFFRACTIONr_mcangle_it3.9294.2981371
X-RAY DIFFRACTIONr_mcangle_other3.9284.31372
X-RAY DIFFRACTIONr_scbond_it2.9063.1591084
X-RAY DIFFRACTIONr_scbond_other2.9013.1591084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6084.5961586
X-RAY DIFFRACTIONr_long_range_B_refined7.38923.5172492
X-RAY DIFFRACTIONr_long_range_B_other7.39123.5182492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.977→2.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 42 -
Rwork0.259 498 -
obs--37.53 %

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