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- PDB-4tnu: Human brain aspartoacylase mutant Y231C complex with intermediate... -

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Basic information

Entry
Database: PDB / ID: 4tnu
TitleHuman brain aspartoacylase mutant Y231C complex with intermediate analog (N-phosphonomethyl-L-aspartate)
ComponentsAspartoacylase
KeywordsHYDROLASE / Canavan disease / Zinc-dependent hydrolase / aspartoacylase family / aminoacylase-2 / N-acetyl-L-aspartate
Function / homology
Function and homology information


aspartoacylase / aspartoacylase activity / aspartate metabolic process / acetate metabolic process / Aspartate and asparagine metabolism / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding ...aspartoacylase / aspartoacylase activity / aspartate metabolic process / acetate metabolic process / Aspartate and asparagine metabolism / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #160 / Aspartoacylase / : / Succinylglutamate desuccinylase/aspartoacylase / AstE/AspA barrel-sandwich hybrid domain / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich ...N-terminal domain of TfIIb - #160 / Aspartoacylase / : / Succinylglutamate desuccinylase/aspartoacylase / AstE/AspA barrel-sandwich hybrid domain / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID / Aspartoacylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E.
CitationJournal: Biochemistry / Year: 2014
Title: Aspartoacylase catalytic deficiency as the cause of canavan disease: a structural perspective.
Authors: Wijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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_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: Aspartoacylase
B: Aspartoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0016
Polymers71,4482
Non-polymers5534
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-15 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.959, 147.959, 103.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 10 - 310 / Label seq-ID: 10 - 310

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

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Components

#1: Protein Aspartoacylase / Aminoacylase-2 / ACY-2


Mass: 35724.051 Da / Num. of mol.: 2 / Mutation: Y231C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPA, ACY2, ASP / Plasmid: pPICZA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P45381, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AS9 / N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID / N-PHOSPHONOMETHYL-L-ASPARTIC ACID / (2S)-2-(HYDROPEROXY(METHOXY)PHOSPHORYLAMINO)SUCCINIC ACID


Type: L-peptide linking / Mass: 211.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG 3350, 0.05M sodium citrate, 0.3M potassium phosphate (dibasic), 3% ethylene glycol, 0.01M DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.283 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25970 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O4H

2o4h


Resolution: 2.9→48.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.541 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.572 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23473 1320 5.1 %RANDOM
Rwork0.19724 ---
obs0.19913 24598 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2--1.59 Å20 Å2
3----3.17 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 28 24 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194974
X-RAY DIFFRACTIONr_bond_other_d0.0030.024760
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.976742
X-RAY DIFFRACTIONr_angle_other_deg0.879311002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7224.483232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50115870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.281524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215560
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021112
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_it3.946.8762412
X-RAY DIFFRACTIONr_mcbond_other3.946.8772413
X-RAY DIFFRACTIONr_mcangle_it6.10610.3093008
X-RAY DIFFRACTIONr_mcangle_other6.10410.313008
X-RAY DIFFRACTIONr_scbond_it3.8177.2032561
X-RAY DIFFRACTIONr_scbond_other3.8167.2032562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.20710.6423735
X-RAY DIFFRACTIONr_long_range_B_refined8.74453.1885381
X-RAY DIFFRACTIONr_long_range_B_other8.74353.1875381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18706 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 103 -
Rwork0.323 1703 -
obs--96.32 %

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