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- PDB-4uu7: Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl... -

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Basic information

Entry
Database: PDB / ID: 4uu7
TitleCrystal structure of zebrafish Sirtuin 5 in complex with 3-methyl- succinylated CPS1-peptide
Components
  • CARBAMOYLPHOSPHATE SYNTHETASE I
  • NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
KeywordsHYDROLASE / SIRTUIN 5 / REGULATORY ENZYME / DEACYLASE / MITOCHONDRIAL / ROSSMANN-FOLD / ZINC-BINDING
Function / homology
Function and homology information


organophosphate metabolic process / carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity ...organophosphate metabolic process / carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / 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 / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / histone deacetylase activity, NAD-dependent / response to growth hormone / cellular response to fibroblast growth factor stimulus / response to food / glutamate binding / heterocyclic compound binding / midgut development / nitric oxide metabolic process / small molecule binding / response to zinc ion / glutamine metabolic process / response to starvation / response to dexamethasone / response to amine / mitochondrial nucleoid / potassium ion binding / NAD+ binding / acyl binding / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / cellular response to glucagon stimulus / 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 / nucleus / metal ion binding / 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 / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Glutamine amidotransferase / Glutamine amidotransferase class-I / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / 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 / ATP-grasp fold / ATP-grasp fold profile. / DHS-like NAD/FAD-binding domain superfamily / 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
(2R)-2-methylbutanedioic acid / (2S)-2-methylbutanedioic 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 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 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references / Other
Revision 1.2Nov 2, 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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 7, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Jan 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

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Assembly

Deposited unit
A: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
B: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
D: CARBAMOYLPHOSPHATE SYNTHETASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,79914
Polymers61,8173
Non-polymers98311
Water73941
1
A: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
D: CARBAMOYLPHOSPHATE SYNTHETASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9098
Polymers31,3932
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-4.1 kcal/mol
Surface area26240 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)87.510, 87.510, 314.380
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-1301-

NA

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.76013, -0.53985, 0.36161), (-0.52307, 0.17822, -0.83345), (0.3855, -0.82268, -0.41784)
Vector: -25.72821, -42.18591, -42.44979)

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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 CARBAMOYLPHOSPHATE SYNTHETASE I


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

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Non-polymers , 8 types, 52 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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / 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: Chemical ChemComp-JO3 / (2R)-2-methylbutanedioic acid


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4
#9: Chemical ChemComp-SUH / (2S)-2-methylbutanedioic acid


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.3 / Details: 22% PEG3350, 0.1 M HEPES PH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 / Details: MIRROR
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15155 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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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→48.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.886 / SU B: 44.939 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL RESIDUES OF PROTEIN CHAINS ARE DISORDERED RESIDUES A280 TO A281 ARE DISORDERED. THE PEPTIDE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL RESIDUES OF PROTEIN CHAINS ARE DISORDERED RESIDUES A280 TO A281 ARE DISORDERED. THE PEPTIDE LYSINE IS MODIFIED BY A 3-METHYL-SUCCINYL,WHICH AUTHORS COULD NOT IDENTIFY TO BE S OR R FROM THE DENSITY. RESIDUES CYS274 OF PROTEIN CHAIN A AND B FORM A SS-BRIDGE
RfactorNum. reflection% reflectionSelection details
Rfree0.27007 740 4.9 %RANDOM
Rwork0.19875 ---
obs0.20222 14414 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 3→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 54 41 4259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194415
X-RAY DIFFRACTIONr_bond_other_d0.0060.024187
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9675969
X-RAY DIFFRACTIONr_angle_other_deg1.2593.0059649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50522.737190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36215702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.711536
X-RAY DIFFRACTIONr_chiral_restr0.0860.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214920
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021012
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_it3.4284.7152175
X-RAY DIFFRACTIONr_mcbond_other3.4294.7132174
X-RAY DIFFRACTIONr_mcangle_it5.4777.0592711
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7365.1372239
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→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 47 -
Rwork0.338 1034 -
obs--100 %
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)
11.34510.30070.21180.32250.25370.498-0.02210.12870.0792-0.0207-0.0281-0.0523-0.044-0.11590.05020.12660.01140.01150.1854-0.04540.0683-22.6051-26.2913-6.305
21.40090.1361-1.00540.32540.52961.99310.0027-0.12840.04710.00330.0904-0.0310.00710.2468-0.09310.127-0.01130.04110.2134-0.05070.0253.0942-29.835-27.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 298
2X-RAY DIFFRACTION2B33 - 298

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