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- PDB-5bwl: Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Su... -

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Basic information

Entry
Database: PDB / ID: 5bwl
TitleCrystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide
Components
  • Coumarin-labelled succinyl peptide
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsHYDROLASE
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 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
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 / molecular replacement / Resolution: 1.548 Å
AuthorsGai, W. / Jiang, H. / Liu, D.
CitationJournal: To be published
Title: Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide
Authors: Gai, W. / Jiang, H. / Liu, D.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,2424
Polymers32,0012
Non-polymers2412
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.420, 55.536, 124.680
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: 31584.936 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Coumarin-labelled succinyl peptide


Mass: 416.470 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 / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris (pH 6.5), 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.548→50 Å / Num. obs: 43833 / % possible obs: 97.7 % / Redundancy: 4.59 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHENIX1.10.1-2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NYR

2nyr


Resolution: 1.548→35.071 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1996 4.67 %RANDOM
Rwork0.2121 ---
obs0.2133 42745 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.548→35.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 14 376 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182146
X-RAY DIFFRACTIONf_angle_d1.4032897
X-RAY DIFFRACTIONf_dihedral_angle_d10.3711707
X-RAY DIFFRACTIONf_chiral_restr0.072310
X-RAY DIFFRACTIONf_plane_restr0.011382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5479-1.58660.30641410.24882891X-RAY DIFFRACTION97
1.5866-1.62950.26951450.2362932X-RAY DIFFRACTION100
1.6295-1.67740.27881420.23322912X-RAY DIFFRACTION100
1.6774-1.73160.28531450.22222940X-RAY DIFFRACTION100
1.7316-1.79340.26211450.22932964X-RAY DIFFRACTION100
1.7934-1.86520.29981440.22142937X-RAY DIFFRACTION100
1.8652-1.95010.30441430.25722942X-RAY DIFFRACTION99
1.9501-2.05290.23851450.20932973X-RAY DIFFRACTION100
2.0529-2.18150.2031430.21332932X-RAY DIFFRACTION99
2.1815-2.34990.23461440.20672921X-RAY DIFFRACTION97
2.3499-2.58640.2491460.19532979X-RAY DIFFRACTION100
2.5864-2.96050.21281460.19752983X-RAY DIFFRACTION99
2.9605-3.72920.20221360.19532775X-RAY DIFFRACTION91
3.7292-35.07970.22361310.21762668X-RAY DIFFRACTION83

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