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- PDB-1asz: THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND... -

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Basic information

Entry
Database: PDB / ID: 1asz
TitleTHE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION
Components
  • ASPARTYL-tRNA SYNTHETASE
  • T-RNA (75-MER)
KeywordsCOMPLEX (AMINOACYL-TRNA SYNTHASE/TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) complex
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / sequence-specific mRNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / 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. ...Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / 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
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Aspartate--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsCavarelli, J. / Rees, B. / Thierry, J.C. / Moras, D.
Citation
Journal: EMBO J. / Year: 1994
Title: The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction.
Authors: Cavarelli, J. / Eriani, G. / Rees, B. / Ruff, M. / Boeglin, M. / Mitschler, A. / Martin, F. / Gangloff, J. / Thierry, J.C. / Moras, D.
#1: Journal: Biochimie / Year: 1993
Title: Yeast Aspartyl-tRNA Synthetase: A Structural View of the Aminoacylation Reaction Aminoacyl-tRNA Synthetase
Authors: Cavarelli, J. / Rees, B. / Thierry, J.C. / Moras, D.
#2: Journal: Nature / Year: 1993
Title: Yeast tRNA Asp Recognition by its Cognate Class II Aminoacyl-tRNA Synthetase
Authors: Cavarelli, J. / Rees, B. / Ruff, M. / Thierry, J.C. / Moras, D.
#3: Journal: Science / Year: 1991
Title: Class II Aminoacyl Transfer RNA Synthetases: Crystal Structure of Yeast Aspartyl-tRNA Synthetase Complexed with tRNA Asp
Authors: Ruff, M. / Krishnaswamy, S. / Boeglin, M. / Poterszman, A. / Mitschler, A. / Podjarny, A. / Rees, B. / Thierry, J.C. / Moras, D.
History
DepositionJan 19, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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

Downloads & links

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Assembly

Deposited unit
R: T-RNA (75-MER)
S: T-RNA (75-MER)
A: ASPARTYL-tRNA SYNTHETASE
B: ASPARTYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4316
Polymers160,4164
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.270, 145.350, 86.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 557 / 2: CIS PROLINE - PRO B 557
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98985, -0.06121, -0.12824), (-0.07636, -0.53199, 0.8433), (-0.11984, 0.84454, 0.52191)
Vector: 142.5, 98.6, -43.15)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 68 .. R 676 B 68 .. S 676 0.91

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Components

#1: RNA chain T-RNA (75-MER)


Mass: 24181.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: aspartate-tRNA ligase
#2: Protein ASPARTYL-tRNA SYNTHETASE


Mass: 56026.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P04802
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.18 %
Crystal
*PLUS
Density % sol: 69 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mMTris-maleate/NaOH1drop
25 mM1dropMgCl2
325 %(w/v)ammonium sulfate1drop
410 mg/mlaspartyl-tRNA synthetase1drop
560 %(w/v)ammonium sulfate1reservoir
64.8 mg/mltRNAAsp1drop

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Data collection

DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 46698 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 3 Å / Num. measured all: 135407

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
MARXDSdata reduction
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 3
Details: TRNA RIBOSES 607, 609, 617, 618, 619, 637, 648, 658, 660, 676, FROM EACH CHAIN, HAVE BEEN CONSTRAINED TO 2' ENDO PUCKER. ALL OTHER TRNA RIBOSES ARE 3' ENDO PUCKER.
RfactorNum. reflection% reflection
Rwork0.203 --
obs0.203 42994 80 %
Displacement parametersBiso mean: 30 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7892 3204 62 0 11158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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