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- PDB-6eo0: Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyc... -

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Basic information

Entry
Database: PDB / ID: 6eo0
TitleZebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29
ComponentsNAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsSIGNALING PROTEIN / Hydrolase / PTM / inhibitor
Function / homology
Function and homology information


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 histone deacetylase activity / acyl binding / heterocyclic compound binding ...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 histone deacetylase activity / acyl binding / heterocyclic compound binding / NAD+ 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 / 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
Chem-BV8 / Chem-BVT / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung04115 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Authors: Rajabi, N. / Auth, M. / Troelsen, K.R. / Pannek, M. / Bhatt, D.P. / Fontenas, M. / Hirschey, M.D. / Steegborn, C. / Madsen, A.S. / Olsen, C.A.
History
DepositionOct 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NAD-dependent protein deacylase sirtuin-5, mitochondrial
D: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14717
Polymers122,7374
Non-polymers6,41013
Water3,171176
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1725
Polymers30,6841
Non-polymers2,4884
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)31,9924
Polymers30,6841
Non-polymers1,3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9924
Polymers30,6841
Non-polymers1,3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9924
Polymers30,6841
Non-polymers1,3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.930, 113.590, 72.310
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA25 - 2974 - 276
21PROPROLEULEUBB25 - 2974 - 276
12PROPROGLUGLUAA25 - 2984 - 277
22PROPROGLUGLUCC25 - 2984 - 277
13PROPROLEULEUAA25 - 2974 - 276
23PROPROLEULEUDD25 - 2974 - 276
14PROPROLEULEUBB25 - 2974 - 276
24PROPROLEULEUCC25 - 2974 - 276
15ASPASPGLUGLUBB24 - 2983 - 277
25ASPASPGLUGLUDD24 - 2983 - 277
16PROPROLEULEUCC25 - 2974 - 276
26PROPROLEULEUDD25 - 2974 - 276

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 30684.156 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 189 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BV8 / 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]carbonimidoyl]amino]propanoic acid


Mass: 1180.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H63N11O19P2S
#5: Chemical
ChemComp-BVT / 3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid


Mass: 1180.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H63N11O19P2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG8000, 0.2 M MgCl2, 0.1 M Tris/HCl pH 8.5, 0.1 M glycine
PH range: 8.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38453 / % possible obs: 96.2 % / Redundancy: 3.8 % / CC1/2: 0.989 / Rrim(I) all: 0.252 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4467 / CC1/2: 0.517 / Rrim(I) all: 1.702 / % possible all: 97.3

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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: 2.4→48.41 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 43.823 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30492 1923 5 %RANDOM
Rwork0.25263 ---
obs0.25531 36530 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å21.44 Å2
2---1.63 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8541 0 420 176 9137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199281
X-RAY DIFFRACTIONr_bond_other_d0.0050.028439
X-RAY DIFFRACTIONr_angle_refined_deg1.9672.00812614
X-RAY DIFFRACTIONr_angle_other_deg1.33.01619611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54251104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80522.565386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.062151438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8151576
X-RAY DIFFRACTIONr_chiral_restr0.10.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110061
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021934
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_it2.0323.8874416
X-RAY DIFFRACTIONr_mcbond_other2.0323.8874417
X-RAY DIFFRACTIONr_mcangle_it3.3285.8235508
X-RAY DIFFRACTIONr_mcangle_other3.3285.8235509
X-RAY DIFFRACTIONr_scbond_it1.9834.1514865
X-RAY DIFFRACTIONr_scbond_other1.9834.1524863
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0786.1547102
X-RAY DIFFRACTIONr_long_range_B_refined6.12245.99210054
X-RAY DIFFRACTIONr_long_range_B_other6.11545.96310042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A165040.1
12B165040.1
21A165240.1
22C165240.1
31A165660.09
32D165660.09
41B164420.09
42C164420.09
51B165380.11
52D165380.11
61C166120.1
62D166120.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 142 -
Rwork0.406 2706 -
obs--97.53 %
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)
10.09850.135-0.0030.6951-0.07070.2737-0.0071-0.02820.0079-0.0229-0.01290.00350.00870.04550.02010.314-0.00730.18380.0253-0.00470.1148.184538.867740.8871
20.0645-0.07860.03050.2318-0.01580.22630.0051-0.0118-0.0220.00660.03410.0409-0.02550.0471-0.03920.34710.00020.1990.01690.00220.124940.038635.364174.7223
30.128-0.0296-0.21410.72780.06470.37420.04460.03520.03850.0290.00790.0075-0.0344-0.059-0.05260.3176-0.01110.17560.0127-0.00470.107616.584538.31233.7975
40.0338-0.13730.0290.70540.13890.47330.00780.0005-0.0006-0.0109-0.01140.01870.0049-0.01780.00360.30250.01320.20210.00130.00860.1368.413236.475267.5814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 298
2X-RAY DIFFRACTION2B24 - 298
3X-RAY DIFFRACTION3C25 - 298
4X-RAY DIFFRACTION4D24 - 298

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