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- PDB-4pv3: Crystal structure of potassium-dependent plant-type L-asparaginas... -

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Basic information

Entry
Database: PDB / ID: 4pv3
TitleCrystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with Na+ cations
Components
  • L-ASPARAGINASE ALPHA SUBUNIT
  • L-ASPARAGINASE BETA SUBUNIT
KeywordsHYDROLASE / metal binding sites / potassium coordination / K-dependent enzyme / Ntn-hydrolase / plant protein / L-asparaginase / isoaspartyl aminopeptidase / amidohydrolase
Function / homology(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / hydrolase activity / Alpha Beta / Isoaspartyl peptidase/L-asparaginase 2
Function and homology information
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBejger, M. / Gilski, M. / Imiolczyk, B. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase
Authors: Bejger, M. / Imiolczyk, B. / Clavel, D. / Gilski, M. / Pajak, A. / Marsolais, F. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of plant asparaginase
Authors: Michalska, K. / Bujacz, G. / Jaskolski, M.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate
Authors: Michalska, K. / Brzezinski, K. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M.
#4: Journal: J.Biol.Chem. / Year: 2008
Title: The mechanism of autocatalytic activation of plant-type L-asparaginases
Authors: Michalska, K. / Hernandez-Santoyo, A. / Jaskolski, M.
#5: Journal: ACTA BIOCHIM.POL. / Year: 2006
Title: Structural aspects of L-asparaginases, their friends and relations
Authors: Michalska, K. / Jaskolski, M.
#6: Journal: Eur.J.Biochem. / Year: 2004
Title: Expression, purification and catalytic activity of Lupinus luteus asparagine -amidohydrolase and its Escherichia coli homolog
Authors: Borek, D. / Michalska, K. / Brzezinski, K. / Kisiel, A. / Podkowi ski, J. / Bonthron, D.T. / Krowarsch, D. / Otlewski, J. / Jaskolski, M.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by Escherichia coli genome
Authors: Borek, D. / Jaskolski, M.
#8: Journal: ACTA BIOCHIM.POL. / Year: 2001
Title: Sequence analysis of enzymes with asparaginase activity
Authors: Borek, D. / Jaskolski, M.
#9: Journal: Biochemistry / Year: 2012
Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis
Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A.
#10: Journal: Chem.Biol. / Year: 2013
Title: Free glicyne accelerates the autoproteolytic activation of human asparaginase
Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / McSorley, T. / Konrad, M. / Lavie, A.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _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: L-ASPARAGINASE ALPHA SUBUNIT
B: L-ASPARAGINASE BETA SUBUNIT
C: L-ASPARAGINASE ALPHA SUBUNIT
D: L-ASPARAGINASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3738
Polymers69,2814
Non-polymers924
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-118 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.403, 103.424, 124.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L-ASPARAGINASE ALPHA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 21015.805 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SUBUNIT ALPHA (UNP residues 1-195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#2: Protein L-ASPARAGINASE BETA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 13624.618 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SUBUNIT BETA (UNP residues 196-326)
Source method: isolated from a genetically manipulated source
Details: SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DIFFERENCE (POLYMORPHISM) AT POSITION 17 REFLECTS A DIFFERENT CULTIVAR (AC COMPASS).

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 0.1M bis tris propane, 0.2M sodium nitrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 14, 2012
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.09→46.55 Å / Num. all: 44381 / Num. obs: 44381 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 43.625 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.78
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.47 / Num. unique all: 7009 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PU6

4pu6


Resolution: 2.09→46.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.743 / SU ML: 0.127 / Isotropic thermal model: ISOTROPIC / Cross valid method: R free / ESU R: 0.159 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 930 2.1 %RANDOM
Rwork0.178 ---
all0.179 43381 --
obs0.179 43381 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.988 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 4 286 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194295
X-RAY DIFFRACTIONr_bond_other_d0.0010.022867
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9285807
X-RAY DIFFRACTIONr_angle_other_deg1.01537018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59424.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58915730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9321531
X-RAY DIFFRACTIONr_chiral_restr0.1140.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.09→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 60 -
Rwork0.252 2910 -
obs-2910 98.15 %
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)
11.1786-0.3064-0.74832.8896-0.83823.64750.0161-0.0430.00050.05980.00990.2575-0.315-0.2698-0.0260.03490.02390.00930.0393-0.02050.057-0.376725.377523.3675
23.2534-0.1748-1.20732.5176-0.5212.677-0.03370.3312-0.1406-0.663-0.0037-0.00260.16620.07380.03740.1767-0.00970.00290.09140.00490.01768.805820.065811.4534
32.4272-1.0387-0.58543.708-0.60262.0509-0.0455-0.1708-0.13420.0831-0.0317-0.0580.19450.14920.07720.03770.00230.01470.03230.03170.12817.9683-6.067831.1232
41.9325-0.7528-0.9723.231-0.98333.39880.088-0.02680.1795-0.3592-0.2821-0.7378-0.06190.75120.1940.09140.01970.06530.23880.090.283219.958-0.508522.0205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 158
2X-RAY DIFFRACTION2B196 - 326
3X-RAY DIFFRACTION3C2 - 156
4X-RAY DIFFRACTION4D196 - 326

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