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- PDB-4pu6: Crystal structure of potassium-dependent plant-type L-asparaginas... -

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Basic information

Entry
Database: PDB / ID: 4pu6
TitleCrystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ 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
Function and homology information


beta-aspartyl-peptidase / hydrolase activity
Similarity search - Function
(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / : / beta-aspartyl-peptidase
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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. / Podkowinski, 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 12, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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)69,5709
Polymers69,2814
Non-polymers2895
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-94 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.938, 102.672, 127.035
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 (common 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 (common bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
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
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 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: 2.3→47.6 Å / Num. obs: 32518 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 57.38 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.97
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.98 / % possible all: 78.8

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEZ

2gez


Resolution: 2.3→47.6 Å / SU ML: 0.27 / Phase error: 27.94 / Stereochemistry target values: ENGH & HUBER / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.231 1009 3.1 %
Rwork0.176 --
obs0.177 32518 96.3 %
all-32518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 13 114 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184313
X-RAY DIFFRACTIONf_angle_d1.4665835
X-RAY DIFFRACTIONf_dihedral_angle_d14.8991565
X-RAY DIFFRACTIONf_chiral_restr0.091673
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.323 111 -
Rwork0.2834 3454 -
obs--76 %
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)
10.7284-0.87540.81731.6448-0.06962.34020.13020.45640.0037-1.0089-0.0337-0.0074-0.0807-0.1107-0.09341.0420.0394-0.04790.34910.00290.2240.769228.23849.7554
21.6650.0244-0.5313.8548-0.60373.18450.18010.00930.0513-0.1769-0.0622-0.1631-0.68210.214-0.09240.3511-0.04690.02940.2278-0.04340.19692.719127.132923.4807
30.4646-0.18450.09031.64170.971.19020.0523-0.4570.27590.60340.0160.5622-0.4903-0.1716-0.06010.5912-0.06220.13030.3515-0.03850.1278-2.800821.695435.3971
45.9161-1.6190.7530.5255-0.69933.08120.030.4542-0.3837-0.472-0.07470.17670.1911-0.0227-0.03990.26770.0838-0.28620.8541-0.09831.1422-18.59816.510717.5464
50.3251-0.5201-0.42632.1929-0.50662.20640.555-0.0669-0.218-0.926-0.2547-0.3421-0.45350.2527-0.13470.3574-0.06290.20870.2955-0.00950.22967.077820.224819.0946
63.57431.2717-0.8174.74350.18894.72960.08490.5768-0.2541-0.7433-0.26040.21680.0819-0.05770.0750.71370.0512-0.03330.3157-0.02230.20873.76939.16813.5253
71.76490.1169-2.94173.5593-0.98615.0748-0.07080.0594-0.1736-0.263-0.1106-0.64670.06330.75460.10670.76430.11380.78030.47090.15560.576517.877914.332211.1185
81.8272-0.4711-0.84421.2384-0.16252.68360.04260.3034-0.0787-0.36120.098-0.2501-0.06930.3502-0.03021.6030.15191.07990.51590.1134-0.729214.737416.74883.0707
91.4817-0.1791-0.182.3182-1.40320.8841-0.252-0.2904-0.2570.0925-0.1946-0.9920.35070.87710.27530.37790.17740.04520.59390.26061.010521.7953-8.35430.6371
102.5225-0.6629-0.18823.47630.01362.2659-0.1395-0.3278-0.8789-0.1686-0.1312-0.75290.03240.4690.22810.38730.08620.09170.37620.22150.701212.185-10.839832.4582
112.7230.05620.29854.8715-0.14423.80420.06510.0186-0.4305-0.7768-0.09040.10640.28560.25560.04680.30450.04460.06980.21410.04280.29983.8393-1.257423.7023
120.6746-0.4401-0.14943.0861-0.44061.3220.1489-0.0935-0.5872-0.3339-0.18180.97680.0702-0.2760.05340.2111-0.0645-0.01170.26850.02150.4257-3.6213-0.249525.6722
136.30771.02065.05432.2340.9635.7479-0.093-0.324-0.22140.7811-0.24770.12280.45930.03070.22030.5185-0.02940.14290.32170.16670.4368-0.6942-6.373940.5643
140.8716-0.83370.18632.7913-2.83653.5687-0.1257-0.25470.07660.22820.2241-0.9556-0.3220.49870.06270.99360.0123-0.40890.83940.26030.684615.22863.135449.74
152.07320.2879-0.76453.3707-1.35492.2889-0.1169-0.0526-0.3623-0.3523-0.2492-1.18820.32510.47510.22360.2050.03160.04920.35970.12870.495313.3811.163224.6332
160.0406-0.00210.00331.5206-1.87652.3085-0.04760.2936-0.047-0.51990.0188-0.3378-0.270.3466-0.01870.84060.12550.5410.61170.20710.782120.46985.229412.451
171.1665-0.4392-0.91760.32151.08664.3424-0.06610.19680.0668-0.32310.0488-0.3125-0.25550.5741-0.00630.61310.14110.59830.94240.34651.453228.29721.938815.8565
181.172-0.50040.82311.2557-0.24273.902-0.45440.10210.2078-0.2909-0.0264-0.3071-0.44790.64850.36150.4417-0.04010.22150.66510.18741.055823.83034.136524.0551
190.0972-0.28290.20490.7692-0.62920.5206-0.0155-0.0015-0.2359-0.58-0.2594-0.73360.33510.64310.13840.28330.21610.32070.86420.37041.564125.4054-9.51224.4596
202.9973-1.31720.75450.8043-0.93691.79280.43330.6607-0.6053-0.53190.0821-0.0050.51740.1284-0.35981.04640.10370.16520.4545-0.11880.27616.384215.27898.101
210.3961-0.4855-0.16870.6454-0.02760.76740.20660.49790.2074-0.801-0.1908-0.4452-0.33610.3275-0.06321.56950.0760.36870.5286-0.00190.04818.362828.39897.0689
222.00289.54963.36317.03331.16912.9621-0.19310.5983-0.0773-1.00630.2825-0.43450.03990.36690.04151.36820.1343-0.05950.62320.1189-0.04240.749930.97093.6103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 196 through 247 )
6X-RAY DIFFRACTION6chain 'B' and (resid 248 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 267 )
8X-RAY DIFFRACTION8chain 'B' and (resid 268 through 282 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 19 )
10X-RAY DIFFRACTION10chain 'C' and (resid 20 through 80 )
11X-RAY DIFFRACTION11chain 'C' and (resid 81 through 103 )
12X-RAY DIFFRACTION12chain 'C' and (resid 104 through 132 )
13X-RAY DIFFRACTION13chain 'C' and (resid 133 through 144 )
14X-RAY DIFFRACTION14chain 'C' and (resid 145 through 158 )
15X-RAY DIFFRACTION15chain 'D' and (resid 196 through 256 )
16X-RAY DIFFRACTION16chain 'D' and (resid 257 through 268 )
17X-RAY DIFFRACTION17chain 'D' and (resid 269 through 282 )
18X-RAY DIFFRACTION18chain 'D' and (resid 283 through 295 )
19X-RAY DIFFRACTION19chain 'D' and (resid 296 through 326 )
20X-RAY DIFFRACTION20chain 'B' and (resid 283 through 295 )
21X-RAY DIFFRACTION21chain 'B' and (resid 296 through 319 )
22X-RAY DIFFRACTION22chain 'B' and (resid 320 through 326 )

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