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- PDB-1r1b: EPRS SECOND REPEATED ELEMENT, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1r1b
TitleEPRS SECOND REPEATED ELEMENT, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsTRNA SYNTHETASEAminoacyl tRNA synthetase
KeywordsLIGASE / TRNA SYNTHETASE (LIGASE) / PROTEIN TRANSCRIPTION
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / RNA stem-loop binding / GAIT complex ...regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / RNA stem-loop binding / GAIT complex / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Glutathione S-transferase, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsCahuzac, B. / Berthonneau, E. / Birlirakis, N. / Mirande, M. / Guittet, E.
CitationJournal: EMBO J. / Year: 2000
Title: A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases.
Authors: Cahuzac, B. / Berthonneau, E. / Birlirakis, N. / Guittet, E. / Mirande, M.
History
DepositionDec 15, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)6,7221
Polymers6,7221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein TRNA SYNTHETASE / Aminoacyl tRNA synthetase / TRNA LIGASE


Mass: 6721.820 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Organ: OVARY CELLS / Production host: Escherichia coli (E. coli)
References: UniProt: Q7SIA2, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121NOESY-HSQC
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DOUBLE-- RESONANCE NMR SPECTROSCOPY ON A 15N-LABELED SAMPLE

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Sample preparation

Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 293.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DIANAstructure solution
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 1

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