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- PDB-1e22: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine... -

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Basic information

Entry
Database: PDB / ID: 1.0E+22
TitleLYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and the non-hydrolysable atp analogue amp-pcp
ComponentsLYSYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / nucleic acid binding / magnesium ion binding ...RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / nucleic acid binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / LYSINE / Lysine--tRNA ligase, heat inducible / Lysine--tRNA ligase, heat inducible
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDesogus, G. / Todone, F. / Brick, P. / Onesti, S.
CitationJournal: Biochemistry / Year: 2000
Title: Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction
Authors: Desogus, G. / Todone, F. / Brick, P. / Onesti, S.
History
DepositionMay 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: LYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,04512
Polymers57,7671
Non-polymers1,27811
Water5,513306
1
A: LYSYL-TRNA SYNTHETASE
hetero molecules

A: LYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,09024
Polymers115,5342
Non-polymers2,55622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area14310 Å2
ΔGint-101 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.020, 142.020, 175.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSYL-TRNA SYNTHETASE


Mass: 57767.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: LYSU / Plasmid: PXLYS5 / Gene (production host): LYSU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2
References: UniProt: P14825, UniProt: P0A8N5*PLUS, lysine-tRNA ligase

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Non-polymers , 5 types, 317 molecules

#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsWHEN THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP IS USED INSTEAD OF ATP THE FIRST STEP OF THE ...WHEN THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP IS USED INSTEAD OF ATP THE FIRST STEP OF THE REACTION DOES NOT OCCUR AND THE RESULTING MODEL SHOWS THE CONFORMATION OF THE ATP SUBSTRATE BEFORE THE REACTION.

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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: 4.8 Å3/Da / Density % sol: 74 %
Description: STRUCTURE WAS SOLVED BY DIFFERENCE FOURIER METHODS USING PHASES FROM 1E1O
Crystal growpH: 6.8
Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5 MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION ...Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5 MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING AMP-PCP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMHEPES1drop
35 mMlysine1drop
42 mMbeta-mercaptoethanol1drop
520 %PEG20001reservoir
60.5 M1reservoirLiCl
70.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.32
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
ReflectionResolution: 2.43→25 Å / Num. obs: 33781 / % possible obs: 84.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 8.1
Reflection shellResolution: 2.43→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.099 / % possible all: 65.1
Reflection
*PLUS
Num. measured all: 120728
Reflection shell
*PLUS
% possible obs: 65.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E1O

1e1o


Resolution: 2.43→12 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ASSIGNMENT OF THE ELECTRON DENSITY PEAKS AS MG2+ IONSIS BASED ON THE POSITIONS OBSERVED FOR METAL IONS WHEN THE ELECTRON-DENSE MN2+ IONS WERE USED
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1347 4 %RANDOM
Rwork0.176 ---
obs0.176 33420 84.7 %-
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.43→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 80 306 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.391.5
X-RAY DIFFRACTIONx_mcangle_it3.662
X-RAY DIFFRACTIONx_scbond_it4.522
X-RAY DIFFRACTIONx_scangle_it6.92.5
LS refinement shellResolution: 2.43→2.54 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.329 127 4.3 %
Rwork0.257 2895 -
obs--65.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.4

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