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- PDB-1fyj: SOLUTION STRUCTURE OF MULTI-FUNCTIONAL PEPTIDE MOTIF-1 PRESENT IN... -

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Entry
Database: PDB / ID: 1fyj
TitleSOLUTION STRUCTURE OF MULTI-FUNCTIONAL PEPTIDE MOTIF-1 PRESENT IN HUMAN GLUTAMYL-PROLYL TRNA SYNTHETASE (EPRS).
ComponentsMULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE
KeywordsLIGASE / helix-turn-helix
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA modification in the nucleus and cytosol ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / GAIT complex / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to type II interferon / cellular response to insulin stimulus / RNA stem-loop binding / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / 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 / : ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / 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 / 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 / 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. / 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 / Helix Hairpins / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsJeong, E.-J. / Hwang, G.-S. / Kim, K.H. / Kim, M.J. / Kim, S. / Kim, K.-S.
CitationJournal: Biochemistry / Year: 2000
Title: Structural analysis of multifunctional peptide motifs in human bifunctional tRNA synthetase: identification of RNA-binding residues and functional implications for tandem repeats.
Authors: Jeong, E.J. / Hwang, G.S. / Kim, K.H. / Kim, M.J. / Kim, S. / Kim, K.S.
History
DepositionOct 2, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: MULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)6,3371
Polymers6,3371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein MULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE


Mass: 6337.256 Da / Num. of mol.: 1 / Fragment: RESIDUES 677-733
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P07814, glutamate-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
131DQF-COSY
141HNHA

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Sample preparation

DetailsContents: ~2mM EPRS-R1 U-15N; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no salt / pH: 5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Delaglio,F.processing
PIPP4.2.5Garretr, D.data analysis
X-PLOR3.851Bunger, A.T.structure solution
X-PLOR3.851Bunger, A.T.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: 814 NOE-derived distance constraints, 91 dihedral angle restraints,29 hydrogen bonds restraints, and 49 J coupling constants are used.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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