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- PDB-4utn: Crystal structure of zebrafish Sirtuin 5 in complex with succinyl... -

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Basic information

Entry
Database: PDB / ID: 4utn
TitleCrystal structure of zebrafish Sirtuin 5 in complex with succinylated CPS1-peptide
Components
  • NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
  • SUCCINYL-CPS1-PEPTIDE
KeywordsHYDROLASE / REGULATORY ENZYME / ROSSMANN-FOLD / ZINC-BINDING
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
NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPannek, M. / Gertz, M. / Steegborn, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors.
Authors: Roessler, C. / Nowak, T. / Pannek, M. / Gertz, M. / Nguyen, G.T. / Scharfe, M. / Born, I. / Sippl, W. / Steegborn, C. / Schutkowski, M.
History
DepositionJul 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
D: SUCCINYL-CPS1-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4258
Polymers61,9163
Non-polymers5095
Water30617
1
A: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
D: SUCCINYL-CPS1-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5573
Polymers31,4922
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-1.9 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8685
Polymers30,4241
Non-polymers4444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.440, 87.440, 314.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.74826, -0.5507, -0.36991), (-0.53361, 0.16831, 0.82882), (-0.39416, 0.81756, -0.4198)
Vector: 25.69092, 42.56148, -42.3867)

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABD

#1: Protein NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL / REGULATORY PROTEIN SIR2 HOMOLOG 5 / SIRTUIN 5


Mass: 30423.785 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, RESIDUES 30-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS
References: UniProt: Q6DHI5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide SUCCINYL-CPS1-PEPTIDE


Mass: 1068.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 5 types, 22 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 / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsBENZOYLATED GLYCINE AT POSITION 1 SUCCINYLATED LYSINE AT POSITION 4

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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.4 / Details: 20% PEG3350, 0.1 M HEPES PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 / Details: MIRROR
RadiationMonochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 15155 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 8.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NYR

2nyr


Resolution: 3→75.73 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 43.64 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. STRUCTURE REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV (2012) LOW RESOLUTION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. STRUCTURE REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV (2012) LOW RESOLUTION REFINEMENT TOOLS IN REFMAC5. ACTA CRYST. D.
RfactorNum. reflection% reflectionSelection details
Rfree0.26672 758 5 %RANDOM
Rwork0.2152 ---
obs0.21782 14400 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.934 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 3→75.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 25 17 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194310
X-RAY DIFFRACTIONr_bond_other_d0.0040.024076
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9655838
X-RAY DIFFRACTIONr_angle_other_deg1.1513.0039399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96122.742186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0915690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3571535
X-RAY DIFFRACTIONr_chiral_restr0.10.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214829
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02987
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_it2.2514.3892138
X-RAY DIFFRACTIONr_mcbond_other2.2514.3872137
X-RAY DIFFRACTIONr_mcangle_it3.736.5772666
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5674.652171
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 53 -
Rwork0.301 1012 -
obs--99.91 %
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)
13.2240.6278-0.41371.7938-0.58211.8371-0.05770.2213-0.2452-0.0112-0.009-0.01040.18640.17840.06670.07860.0342-0.0190.16680.05950.087722.584626.392-6.3676
23.1141-0.12111.31671.4534-0.96584.8664-0.025-0.283-0.18770.05340.23250.19060.0821-0.5493-0.20750.11980.0154-0.06210.16450.07040.0915-3.060929.7145-27.3837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 298
2X-RAY DIFFRACTION2B33 - 298

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