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- PDB-6enx: Zebrafish Sirt5 in complex with stalled bicyclic intermediate of ... -

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Basic information

Entry
Database: PDB / ID: 6enx
TitleZebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10
ComponentsNAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsSIGNALING PROTEIN / Hydrolase / PTM / inhibitor / Sirtuin
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 / acyl binding / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 ...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-BJW / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3764
Polymers30,0531
Non-polymers1,3233
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric peak in gelfiltration with slight dimeric shoulder
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint4 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.470, 38.250, 75.550
Angle α, β, γ (deg.)90.00, 122.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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Components

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


Mass: 30053.471 Da / Num. of mol.: 1
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BJW / 4-[(2~{R},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]butanoic acid


Mass: 1179.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H64N10O19P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.36 Å3/Da / Density % sol: 47.9 % / Description: Small cubes
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: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20704 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.989 / Rrim(I) all: 0.213 / Net I/σ(I): 6.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1518 / CC1/2: 0.463 / Rrim(I) all: 1.565 / % possible all: 99.2

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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: 1.95→49.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.995 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24169 1037 5 %RANDOM
Rwork0.19467 ---
obs0.19706 19704 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.588 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å20.21 Å2
2--0.12 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 85 173 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192241
X-RAY DIFFRACTIONr_bond_other_d0.0040.022042
X-RAY DIFFRACTIONr_angle_refined_deg1.9712.0013050
X-RAY DIFFRACTIONr_angle_other_deg1.1623.0144741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33722.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05815347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3551518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
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_it1.912.4611077
X-RAY DIFFRACTIONr_mcbond_other1.912.461078
X-RAY DIFFRACTIONr_mcangle_it2.7313.6871345
X-RAY DIFFRACTIONr_mcangle_other2.733.6861346
X-RAY DIFFRACTIONr_scbond_it2.6912.7691164
X-RAY DIFFRACTIONr_scbond_other2.6932.7711162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1834.0041704
X-RAY DIFFRACTIONr_long_range_B_refined5.52929.482471
X-RAY DIFFRACTIONr_long_range_B_other5.52829.4732472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 75 -
Rwork0.369 1442 -
obs--99.87 %

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