Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA synthetase, Lysine--tRNA ligase
GI: 1932759780
UniProt: P0A8N5
Structures: | 1E1O | 1E1T | 1E22 | 1E24 | 1LYL | 5YZX |
Alpha Fold Predicted Structure: AF-P0A8N5-F1
Enzyme type: ligase


PDB Structures:


1E1O

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid carboxylate group and the tRNA acceptor stem is supplied by coupling the reaction to the hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to the family of class II synthetases and carries out a two-step reaction, in which lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. Crystals of the thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1 A resolution have been used to determine crystal structures of the enzyme in the presence of lysine, the lysyl-adenylate intermediate, and the nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained from crystals soaked in a solution containing ATP and Mn(2+). The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilize the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding.

Download RCSB-PDB Structures:

Pdb Files   1E1O.pdb   1E1T.pdb   1E22.pdb   1E24.pdb   1LYL.pdb   5YZX.pdb  
Pdbx/mmCIF Files   1E1O.cif   1E1T.cif   1E22.cif   1E24.cif   1LYL.cif   5YZX.cif  


Protein sequence:

MSEQETRGANEAIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK

Comments:

Converts ATP to diadenosine tri- and tetraphosphates (Ap(3)A/Ap(4)A) in the presence of L-lysine/Mg(2+)/Zn(2+)





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S E Q E T R G A N E A I D F N D E L R N R R E K L A A L R Q Q G V A F P N D F R R D H T S D Q L H E E F D A K D N Q E L E S L N I E V S V A G R M M T R R I M G K A S F V T L Q D V G G R I Q L Y V A R D S L P E G V Y N D Q F K K W D L G D I I G A R G T L F K T Q T G E L S I H C T E L R L L T K A L R P L P D K F H G L Q D Q E V R Y R Q R Y L D L I A N D K S R Q T F V V R S K I L A A I R Q F M V A R G F M E V E T P M M Q V I P G G A S A R P F I T H H N A L D L D M Y L R I A P E L Y L K R L V V G G F E R V F E I N R N F R N E G I S V R H N P E F T M M E L Y M A Y A D Y H D L I E L T E S L F R T L A Q E V L G T T K V T Y G E H V F D F G K P F E K L T M R E A I K K Y R P E T D M A D L D N F D A A K A L A E S I G I T V E K S W G L G R I V T E I F D E V A E A H L I Q P T F I T E Y P A E V S P L A R R N D V N P E I T D R F E F F I G G R E I G N G F S E L N D A E D Q A E R F Q E Q V N A K A A G D D E A M F Y D E D Y V T A L E Y G L P P T A G L G I G I D R M I M L F T N S H T I R D V I L F P A M R P Q K

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P0A8N5-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0A8N5-F1.cif  
DSSP Secondary Structures   P0A8N5.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. S Onesti,A D Miller,P Brick Structure [details] 7735833 -
Stresses that Raise NpA Levels Induce Protective Nucleoside Tetraphosphate Capping of Bacterial RNA. Daniel J Luciano,Rose Levenson-Palmer,Joel G Belasco Mol Cell [details] 31178354 -