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- PDB-6ljm: Crystal structure of human Sirt5 in complex with the fluorogenic ... -

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Basic information

Entry
Database: PDB / ID: 6ljm
TitleCrystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13
Components
  • ACE-SER-LEU-GLY-SLL
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsTRANSFERASE / Sirt5 / inhibitor / HYDROLASE
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 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to ischemia / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
7-AMINO-4-METHYL-CHROMEN-2-ONE / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsChen, Q. / Yu, Y.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery.
Authors: Yang, L.L. / Wang, H.L. / Yan, Y.H. / Liu, S. / Yu, Z.J. / Huang, M.Y. / Luo, Y. / Zheng, X. / Yu, Y. / Li, G.B.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 5, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free_error / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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: ACE-SER-LEU-GLY-SLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3394
Polymers30,0982
Non-polymers2412
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint6 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)42.200, 55.275, 124.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 29568.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXA8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide ACE-SER-LEU-GLY-SLL


Mass: 529.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.779→50 Å / Num. obs: 28767 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.7 Å2 / Net I/σ(I): 18.46
Reflection shellResolution: 1.78→1.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XHS

5xhs


Resolution: 1.78→41.34 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.11
RfactorNum. reflection% reflection
Rfree0.197 1454 5.12 %
Rwork0.165 --
obs0.166 28384 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.65 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 14 290 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012207
X-RAY DIFFRACTIONf_angle_d1.4322989
X-RAY DIFFRACTIONf_dihedral_angle_d14.9371285
X-RAY DIFFRACTIONf_chiral_restr0.058314
X-RAY DIFFRACTIONf_plane_restr0.007395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7793-1.84280.23861350.20782411X-RAY DIFFRACTION90
1.8428-1.91660.24061430.18612624X-RAY DIFFRACTION98
1.9166-2.00390.22041340.16932684X-RAY DIFFRACTION100
2.0039-2.10950.2091550.1632698X-RAY DIFFRACTION100
2.1095-2.24170.21141330.15152696X-RAY DIFFRACTION100
2.2417-2.41470.16591530.15172692X-RAY DIFFRACTION100
2.4147-2.65770.18581450.16292731X-RAY DIFFRACTION100
2.6577-3.04220.20871600.16342720X-RAY DIFFRACTION100
3.0422-3.83240.19331550.15392765X-RAY DIFFRACTION100
3.8324-41.3360.18121410.1712909X-RAY DIFFRACTION99

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