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- PDB-5ojo: Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglut... -

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Basic information

Entry
Database: PDB / ID: 5ojo
TitleSirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-CPS1 peptide
Components
  • Carbamoyl-phosphate synthase [ammonia], mitochondrial
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsSIGNALING PROTEIN / Sirtuin / Sirt5 / Deacylase / Mitochondria
Function / homology
Function and homology information


carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process / modified amino acid binding ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process / modified amino acid binding / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / homocysteine metabolic process / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / NAD-dependent histone deacetylase activity / hepatocyte differentiation / cellular response to fibroblast growth factor stimulus / response to growth hormone / acyl binding / glutamate binding / response to food / midgut development / nitric oxide metabolic process / response to zinc ion / heterocyclic compound binding / response to starvation / response to dexamethasone / glutamine metabolic process / cellular response to glucagon stimulus / mitochondrial nucleoid / response to amine / potassium ion binding / small molecule binding / NAD+ binding / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / cellular response to cAMP / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / response to toxic substance / vasodilation / transferase activity / endopeptidase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class III / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain ...Sirtuin, class III / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Glutamine amidotransferase class-I / Glutamine amidotransferase / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / TPP-binding domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / DHS-like NAD/FAD-binding domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbamoyl-phosphate synthase [ammonia], mitochondrial / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung Germany
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Authors: Pannek, M. / Simic, Z. / Fuszard, M. / Meleshin, M. / Rotili, D. / Mai, A. / Schutkowski, M. / Steegborn, C.
History
DepositionJul 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn
Revision 1.2Feb 7, 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: Carbamoyl-phosphate synthase [ammonia], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4929
Polymers61,9603
Non-polymers5326
Water1,06359
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
C: Carbamoyl-phosphate synthase [ammonia], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7425
Polymers31,5362
Non-polymers2063
Water362
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)30,7504
Polymers30,4241
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.540, 87.540, 316.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-303-

NA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 34 - 298 / Label seq-ID: 11 - 275

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

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Components

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

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


Mass: 30423.785 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 Carbamoyl-phosphate synthase [ammonia], mitochondrial / Carbamoyl-phosphate synthetase I / CPSase I


Mass: 1112.230 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal benzoylated glycine. HMG-modified lysine
Source: (synth.) Homo sapiens (human)
References: UniProt: P31327, carbamoyl-phosphate synthase (ammonia)

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Non-polymers , 6 types, 65 molecules

#3: 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
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES pH 7.6 20% PEG3350 / PH range: 7.0-8.0

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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 6M / Detector: PIXEL / Date: Sep 8, 2015 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13919 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.248 / Net I/σ(I): 10.2
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1214 / CC1/2: 0.598 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTV

4utv


Resolution: 3.1→48.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.877 / SU B: 45.042 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 713 5.1 %RANDOM
Rwork0.196 ---
obs0.2 13206 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 26 59 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194441
X-RAY DIFFRACTIONr_bond_other_d0.0030.024094
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9656016
X-RAY DIFFRACTIONr_angle_other_deg1.1093.0059497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86822.746193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86215706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2151536
X-RAY DIFFRACTIONr_chiral_restr0.0870.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02925
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_it1.6774.8282186
X-RAY DIFFRACTIONr_mcbond_other1.6764.8262185
X-RAY DIFFRACTIONr_mcangle_it2.9127.2322727
X-RAY DIFFRACTIONr_mcangle_other2.9117.2352728
X-RAY DIFFRACTIONr_scbond_it1.895.0682254
X-RAY DIFFRACTIONr_scbond_other1.8895.072255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8857.5253287
X-RAY DIFFRACTIONr_long_range_B_refined5.10255.3734644
X-RAY DIFFRACTIONr_long_range_B_other5.09855.3814643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15996 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 46 -
Rwork0.314 941 -
obs--99.9 %
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)
13.43811.1173-0.25741.8553-0.20051.46560.03090.2603-0.32570.0735-0.0158-0.18020.05610.1933-0.01510.07680.0142-0.03830.07840.00210.092422.00925.9114-6.2547
23.16030.31030.94512.501-0.99964.5163-0.0388-0.1886-0.10790.14660.28430.2304-0.0409-0.7157-0.24550.08430.0607-0.0330.18930.0470.0773-3.500629.203-27.4682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 298
2X-RAY DIFFRACTION2B34 - 298

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