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- PDB-6fky: Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzy... -

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Basic information

Entry
Database: PDB / ID: 6fky
TitleCrystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide
Components
  • 3(R)-(phenylthio)succinyl-CPS1 peptide
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsSIGNALING PROTEIN / Sirtuin 5 / Inhibitor / Deacylase
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / 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 / histone deacetylase activity, NAD-dependent / heterocyclic compound binding ...Transcriptional activation of mitochondrial biogenesis / 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 / histone deacetylase activity, NAD-dependent / heterocyclic compound binding / NAD+ binding / acyl binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / 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 ...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
(2~{S})-2-(phenylmethylsulfanyl)butanedioic acid / (2~{R})-2-(phenylmethylsulfanyl)butanedioic acid / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung04115 Germany
CitationJournal: J. Med. Chem. / Year: 2018
Title: Potent and Selective Inhibitors of Human Sirtuin 5.
Authors: Kalbas, D. / Liebscher, S. / Nowak, T. / Meleshin, M. / Pannek, M. / Popp, C. / Alhalabi, Z. / Bordusa, F. / Sippl, W. / Steegborn, C. / Schutkowski, M.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: NAD-dependent protein deacylase sirtuin-5, mitochondrial
C: 3(R)-(phenylthio)succinyl-CPS1 peptide
I: 3(R)-(phenylthio)succinyl-CPS1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,86311
Polymers64,9284
Non-polymers9357
Water99155
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
C: 3(R)-(phenylthio)succinyl-CPS1 peptide
I: 3(R)-(phenylthio)succinyl-CPS1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9796
Polymers33,4333
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8845
Polymers31,4951
Non-polymers3894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.134, 87.134, 316.677
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 35 - 298 / Label seq-ID: 14 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCI

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


Mass: 31495.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sirt5, si:ch211-121a2.1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DHI5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide 3(R)-(phenylthio)succinyl-CPS1 peptide


Mass: 969.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 7 types, 62 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-E9N / (2~{R})-2-(phenylmethylsulfanyl)butanedioic acid


Mass: 240.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O4S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-DZK / (2~{S})-2-(phenylmethylsulfanyl)butanedioic acid


Mass: 240.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O4S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.4, 20% PEG3350 / PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2016 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 15459 / % possible obs: 99.8 % / Redundancy: 15.5 % / CC1/2: 0.994 / Rrim(I) all: 0.358 / Net I/σ(I): 9.8
Reflection shellResolution: 2.98→3.16 Å / Redundancy: 16 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2399 / CC1/2: 0.513 / Rrim(I) all: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4utv

4utv


Resolution: 2.98→48.51 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.871 / SU B: 44.548 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27485 773 5 %RANDOM
Rwork0.19785 ---
obs0.20163 14686 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.98→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 52 55 4339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194410
X-RAY DIFFRACTIONr_bond_other_d0.0020.024064
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9695967
X-RAY DIFFRACTIONr_angle_other_deg1.0993.0069425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39122.804189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04915699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6271535
X-RAY DIFFRACTIONr_chiral_restr0.10.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214870
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02919
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_it3.0155.5872173
X-RAY DIFFRACTIONr_mcbond_other3.0155.5852172
X-RAY DIFFRACTIONr_mcangle_it4.9988.3662708
X-RAY DIFFRACTIONr_mcangle_other4.9978.3682709
X-RAY DIFFRACTIONr_scbond_it3.1825.9682236
X-RAY DIFFRACTIONr_scbond_other3.1825.9692237
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1668.8143259
X-RAY DIFFRACTIONr_long_range_B_refined7.58664.5354629
X-RAY DIFFRACTIONr_long_range_B_other7.58364.5464628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15972 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.978→3.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 54 -
Rwork0.361 1024 -
obs--97.82 %
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)
11.15930.6803-0.34840.843-0.44740.4164-0.07420.0933-0.0205-0.00080.00620.04370.05290.09530.0680.08430.02040.01210.1010.04850.064422.847426.095-6.2742
21.03610.17640.70220.222-0.39871.88730.0011-0.0354-0.02860.01940.05320.0062-0.0246-0.1625-0.05430.09530.0032-0.04040.11080.03460.0291-2.946329.7119-27.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 298
2X-RAY DIFFRACTION2B33 - 298

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