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Basic information

Entry
Database: PDB / ID: 3ab4
TitleCrystal structure of feedback inhibition resistant mutant of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine
Components(Aspartokinase) x 2
KeywordsTRANSFERASE / aspartate kinase / concerted inhibition / Alternative initiation / Amino-acid biosynthesis / ATP-binding / Diaminopimelate biosynthesis / Kinase / Lysine biosynthesis / Nucleotide-binding
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytosol
Similarity search - Function
Aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like / ACT domain ...Aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like / ACT domain / Carbamate kinase / Acetylglutamate kinase-like / ACT domain profile. / ACT domain / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / THREONINE / Aspartokinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsYoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum
Authors: Yoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Structural Insight into concerted inhibition of alpha 2 beta 2-type aspartate kinase from Corynebacterium glutamicum
Authors: Yoshida, A. / Tomita, T. / Kurihara, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
History
DepositionNov 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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: Aspartokinase
B: Aspartokinase
C: Aspartokinase
D: Aspartokinase
E: Aspartokinase
F: Aspartokinase
G: Aspartokinase
H: Aspartokinase
I: Aspartokinase
J: Aspartokinase
K: Aspartokinase
L: Aspartokinase
M: Aspartokinase
N: Aspartokinase
O: Aspartokinase
P: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,36439
Polymers514,42816
Non-polymers2,93623
Water6,972387
1
A: Aspartokinase
B: Aspartokinase
C: Aspartokinase
D: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,37810
Polymers128,6074
Non-polymers7716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-73 kcal/mol
Surface area40640 Å2
MethodPISA
2
E: Aspartokinase
F: Aspartokinase
G: Aspartokinase
H: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,37810
Polymers128,6074
Non-polymers7716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-71 kcal/mol
Surface area38790 Å2
MethodPISA
3
I: Aspartokinase
J: Aspartokinase
K: Aspartokinase
L: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2319
Polymers128,6074
Non-polymers6245
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-75 kcal/mol
Surface area39900 Å2
MethodPISA
4
M: Aspartokinase
N: Aspartokinase
O: Aspartokinase
P: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,37810
Polymers128,6074
Non-polymers7716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-71 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.033, 112.874, 120.009
Angle α, β, γ (deg.)76.03, 71.07, 74.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aspartokinase / Aspartate kinase


Mass: 44858.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: lysC / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: P26512, aspartate kinase
#2: Protein
Aspartokinase / Aspartate kinase


Mass: 19444.848 Da / Num. of mol.: 8 / Fragment: ACT 1/2 domains, UNP residues 251-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: lysC / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: P26512, aspartate kinase
#3: Chemical
ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE RESIDUES AT 301 IN CHAIN A,C,E,G,I,K,M,O AND 52 IN CHAIN B,D,F,H,J,L,N,P ARE INTRODUCED BY ...THESE RESIDUES AT 301 IN CHAIN A,C,E,G,I,K,M,O AND 52 IN CHAIN B,D,F,H,J,L,N,P ARE INTRODUCED BY SITE-DIRECTED MUTAGENESIS ARTIFICIALLY.

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 0.05M Sodium citrate, 0.1M Ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 15, 2009 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 166233 / % possible obs: 96.3 % / Redundancy: 2 % / Biso Wilson estimate: 67.4 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.5
Reflection shellResolution: 2.47→2.52 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.363 / % possible all: 93.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AAW

3aaw


Resolution: 2.47→39.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.896 / SU B: 26.493 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28769 8052 5 %RANDOM
Rwork0.22297 ---
obs0.22621 151988 95.69 %-
all-167445 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.01 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.393 Å
Refinement stepCycle: LAST / Resolution: 2.47→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30385 0 198 387 30970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02230827
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219862
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.97641789
X-RAY DIFFRACTIONr_angle_other_deg0.897348872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41154077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37925.2191232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.631155203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.15115199
X-RAY DIFFRACTIONr_chiral_restr0.0710.25183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0234522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025573
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_it0.4121.520569
X-RAY DIFFRACTIONr_mcbond_other0.0621.58450
X-RAY DIFFRACTIONr_mcangle_it0.779232851
X-RAY DIFFRACTIONr_scbond_it1.125310258
X-RAY DIFFRACTIONr_scangle_it1.9364.58938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.471→2.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 550 -
Rwork0.305 10031 -
obs--86.12 %
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)
10.4259-0.13940.05610.278-0.11482.3533-0.09790.156-0.0680.0016-0.0126-0.0245-0.1530.1170.11050.0851-0.03180.05520.0789-0.00710.0683-14.972734.871818.7552
22.52451.1216-0.68372.5671-0.12021.32070.0088-0.12620.07180.178-0.0075-0.0346-0.1119-0.068-0.00130.12720.05480.02920.03430.00730.0187-21.444439.19242.089
30.62940.31770.11580.43480.66912.08110.0346-0.105-0.07850.0493-0.0076-0.11170.0522-0.1328-0.0270.08990.01840.00030.1472-0.01970.070422.109232.2518-18.4682
43.5047-0.70920.53093.71470.3293.1649-0.18450.20780.3104-0.24340.151-0.2703-0.42150.23880.03350.1427-0.09620.02990.068-0.01420.05429.562137.4621-41.6979
50.7460.06120.51452.05530.80081.0102-0.0872-0.0495-0.0604-0.2129-0.13110.2074-0.0944-0.04870.21820.13450.01740.03650.1735-0.00270.1209-24.127518.983-31.8861
60.27750.31860.22692.23040.59540.8711-0.2249-0.00840.1906-0.575-0.2190.3829-0.6808-0.16980.44390.54870.144-0.35990.1285-0.05340.2573-30.720642.1857-33.836
70.3935-0.70420.03992.3940.31990.3708-0.0296-0.05460.02030.17290.0203-0.1061-0.00030.02150.00930.077-0.04520.05220.19760.03280.111613.1744-13.6569-39.9137
83.9959-0.61570.9124.0448-0.76212.9126-0.02440.1585-0.2521-0.1098-0.0321-0.31980.3389-0.00040.05650.0833-0.02330.05070.0221-0.02470.075419.5156-38.5821-44.3737
90.646-0.41730.89150.9978-1.2683.13070.0442-0.1217-0.1327-0.11920.16130.18140.1634-0.2046-0.20540.0496-0.03460.02220.12670.00750.0957-25.3455-30.7028-13.4362
103.8818-2.10170.30074.0169-0.06813.85990.17120.2266-0.4656-0.4786-0.03340.19790.3593-0.5928-0.13790.1351-0.1406-0.06310.27090.06040.1205-41.8618-31.2601-35.1863
110.8954-0.22530.32530.4063-0.00331.53250.11480.2103-0.0529-0.0969-0.02670.04140.11850.0065-0.08810.05910.02150.02650.1036-0.03090.107820.3299-36.563512.2012
122.44850.68050.51632.26980.17741.91510.0342-0.0557-0.12110.09770.02340.00410.22230.0565-0.05760.05610.02720.0390.0698-0.01840.124429.9903-43.434533.2899
130.5820.62190.07851.75440.45430.64770.08050.05670.10030.1014-0.02380.051-0.0148-0.099-0.05670.04850.02690.07530.07380.040.1259-16.3655-15.140937.2419
142.50160.25330.51912.21190.4171.82180.11120.0308-0.09920.2267-0.07230.01510.2418-0.0239-0.03890.1086-0.02420.06120.07920.01030.0856-27.0903-37.478539.9398
150.590.9712-0.14241.8494-0.35040.2507-0.07060.0861-0.06260.09610.0913-0.0687-0.04690.0135-0.02070.1994-0.00440.00340.0922-0.01310.216326.42189.600833.1116
163.74640.3095-0.20933.9537-1.32055.8337-0.0074-0.1495-0.0720.725-0.0857-0.0317-0.47280.09260.09310.3041-0.0592-0.10890.01980.03160.066339.194833.811432.5673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 408
2X-RAY DIFFRACTION2B5 - 164
3X-RAY DIFFRACTION3C2 - 409
4X-RAY DIFFRACTION4D3 - 157
5X-RAY DIFFRACTION5E2 - 409
6X-RAY DIFFRACTION6F4 - 156
7X-RAY DIFFRACTION7G2 - 407
8X-RAY DIFFRACTION8H6 - 158
9X-RAY DIFFRACTION9I2 - 406
10X-RAY DIFFRACTION10J9 - 153
11X-RAY DIFFRACTION11K2 - 408
12X-RAY DIFFRACTION12L2 - 159
13X-RAY DIFFRACTION13M2 - 408
14X-RAY DIFFRACTION14N4 - 158
15X-RAY DIFFRACTION15O2 - 407
16X-RAY DIFFRACTION16P5 - 157

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