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- PDB-2d32: Crystal Structure of Michaelis Complex of gamma-Glutamylcysteine ... -

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Basic information

Entry
Database: PDB / ID: 2d32
TitleCrystal Structure of Michaelis Complex of gamma-Glutamylcysteine Synthetase
ComponentsGlutamate--cysteine ligase
KeywordsLIGASE / glutathione homeostasis / peptide synthesis / phosphoryl transfer
Function / homology
Function and homology information


glutamate-cysteine ligase / glutamate-cysteine ligase activity / cellular response to mercury ion / glutathione biosynthetic process / cellular response to arsenic-containing substance / hyperosmotic response / ATP binding / metal ion binding / cytosol
Similarity search - Function
Helix Hairpins - #800 / Glutamate--cysteine ligase, monofunctional / Glutamate--cysteine ligase / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helix Hairpins / Helix non-globular / Special ...Helix Hairpins - #800 / Glutamate--cysteine ligase, monofunctional / Glutamate--cysteine ligase / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helix Hairpins / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CYSTEINE / GLUTAMIC ACID / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHibi, T. / Nakayama, M. / Nii, H. / Kurokawa, Y. / Katano, H. / Oda, J.
Citation
Journal: To be Published
Title: Structural basis of efficient coupling peptide ligation and ATP hydrolysis by gamma-gluatamylcysteine synthetase
Authors: Hibi, T. / Nakayama, M. / Nii, H. / Kurokawa, Y. / Katano, H. / Oda, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.
Authors: Hibi, T. / Nii, H. / Nakatsu, T. / Kimura, A. / Kato, H. / Hiratake, J. / Oda, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Escherichia coli B gamma-glutamylcysteine synthetase: modification, purification, crystallization and preliminary crystallographic analysis.
Authors: Hibi, T. / Hisada, H. / Nakatsu, T. / Kato, H. / Oda, J.
History
DepositionSep 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glutamate--cysteine ligase
B: Glutamate--cysteine ligase
C: Glutamate--cysteine ligase
D: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,48929
Polymers233,0754
Non-polymers3,41425
Water14,412800
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-148 kcal/mol
Surface area73380 Å2
MethodPISA
2
A: Glutamate--cysteine ligase
B: Glutamate--cysteine ligase
C: Glutamate--cysteine ligase
D: Glutamate--cysteine ligase
hetero molecules

A: Glutamate--cysteine ligase
B: Glutamate--cysteine ligase
C: Glutamate--cysteine ligase
D: Glutamate--cysteine ligase
hetero molecules

A: Glutamate--cysteine ligase
B: Glutamate--cysteine ligase
C: Glutamate--cysteine ligase
D: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,46887
Polymers699,22612
Non-polymers10,24275
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area46170 Å2
ΔGint-464 kcal/mol
Surface area215180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)325.530, 325.530, 105.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutamate--cysteine ligase / Gamma-glutamylcysteine synthetase / Gamma-ECS / GCS


Mass: 58268.844 Da / Num. of mol.: 4 / Mutation: C106S, C164S, C205S, C223S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gshI / Plasmid: pKGC20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6W9, glutamate-cysteine ligase

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Non-polymers , 5 types, 825 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 4.77 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium formate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→43.6 Å / Num. obs: 162223 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2 / Num. unique all: 23722 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4G

1v4g


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.086 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19844 8122 5 %RANDOM
Rwork0.16841 ---
obs0.16994 154095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15828 0 205 800 16833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216364
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.97522188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58951993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5523.469764
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.266152705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.29915134
X-RAY DIFFRACTIONr_chiral_restr0.0860.22416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212480
X-RAY DIFFRACTIONr_nbd_refined0.2130.37478
X-RAY DIFFRACTIONr_nbtor_refined0.3170.511285
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.51714
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.539
X-RAY DIFFRACTIONr_mcbond_it1.548210277
X-RAY DIFFRACTIONr_mcangle_it2.376316064
X-RAY DIFFRACTIONr_scbond_it1.86926961
X-RAY DIFFRACTIONr_scangle_it2.58436124
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 578 -
Rwork0.213 11389 -
obs-11389 100 %

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