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- PDB-4utx: Crystal structure of zebrafish Sirtuin 5 in complex with 3-nitro-... -

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Basic information

Entry
Database: PDB / ID: 4utx
TitleCrystal structure of zebrafish Sirtuin 5 in complex with 3-nitro- propionylated CPS1-peptide
Components
  • CARBAMOYLPHOSPHATE SYNTHETASE I
  • NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
KeywordsHYDROLASE / REGULATORY ENZYME / DEACYLASE / MITOCHONDRIAL / ROSSMANN-FOLD / ZINC-BINDING
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 / nitric oxide metabolic process / 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 / response to zinc ion / heterocyclic compound binding / response to dexamethasone / response to starvation / glutamine metabolic process / mitochondrial nucleoid / cellular response to glucagon stimulus / 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 / mitochondrial inner membrane / response to lipopolysaccharide / 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
3-NITROPROPANOIC ACID / Carbamoyl-phosphate synthase [ammonia], mitochondrial / carbamoyl-phosphate synthase (ammonia) / 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. / 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 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references / Other
Revision 1.2Dec 7, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: CARBAMOYLPHOSPHATE SYNTHETASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59212
Polymers61,8173
Non-polymers7769
Water61334
1
A: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
C: CARBAMOYLPHOSPHATE SYNTHETASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7026
Polymers31,3932
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8.6 kcal/mol
Surface area15640 Å2
MethodPISA
2
B: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8916
Polymers30,4241
Non-polymers4675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 87.490, 313.790
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-1303-

NA

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.75668, -0.5427, 0.36458), (-0.52439, 0.17076, -0.83418), (0.39045, -0.82239, -0.4138)
Vector: -26.13046, -42.64455, -42.20502)

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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 / SIRTUIN 5 / REGULATORY PROTEIN SIR2 HOMOLOG 5


Mass: 30423.785 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, UNP 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 CARBAMOYLPHOSPHATE SYNTHETASE I / 3-NITRO-PROPIONYL-CPS1 PEPTIDE


Mass: 969.112 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 524-531 / Source method: obtained synthetically
Details: BENZOYLATED GLYCINE AT POSITION 1. 3-NITRO-PROPIONYLATED LYSINE AT POSITION 4
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5R209, UniProt: P31327*PLUS

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Non-polymers , 7 types, 43 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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
#6: 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
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-3NP / 3-NITROPROPANOIC ACID / Beta-Nitropropionic acid


Mass: 119.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL RESIDUES GIDPFT ARE ENCODED ON PET151 EXPRESSION VECTOR AND DO NOT BELONG TO THE NATIVE PROTEIN

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5 / Details: 22% PEG3350, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91705
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91705 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13762 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 14.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NYR

2nyr


Resolution: 3.1→48.38 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / SU B: 45.245 / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL PROTEIN RESIDUES ARE DISORDERED. RESIDUES A280 TO A281 ARE DISORDERED. RESIDUES B275 TO B280 ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL PROTEIN RESIDUES ARE DISORDERED. RESIDUES A280 TO A281 ARE DISORDERED. RESIDUES B275 TO B280 ARE DISORDERED. PROTEIN RESIDUES CYS274 OF CHAIN A AND B FORM A DISULFIDE BRIDGE
RfactorNum. reflection% reflectionSelection details
Rfree0.26189 714 5.2 %RANDOM
Rwork0.19357 ---
obs0.19722 13048 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.991 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----4.58 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4118 0 41 34 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194268
X-RAY DIFFRACTIONr_bond_other_d0.0050.024042
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9635768
X-RAY DIFFRACTIONr_angle_other_deg1.1663.0039318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13722.826184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92715684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3621534
X-RAY DIFFRACTIONr_chiral_restr0.0820.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214752
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02973
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_it4.0185.4852115
X-RAY DIFFRACTIONr_mcbond_other4.0185.4842114
X-RAY DIFFRACTIONr_mcangle_it6.4218.2112635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3035.9482151
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: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 42 -
Rwork0.304 930 -
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)
10.02980.03070.01660.03210.01660.018-0.00450.0072-0.0599-0.00550.0145-0.0647-0.0068-0.0324-0.010.04780.0014-0.00260.1538-0.09040.1671-22.8244-26.2668-6.2798
20.5722-0.0173-0.6490.00120.01960.7361-0.0401-0.0226-0.01880.00330.00940.00990.05460.02250.03060.1029-0.02350.080.0894-0.0590.17813.2455-30.0096-26.7052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 298
2X-RAY DIFFRACTION2B33 - 298

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