Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA glutamyl-Q(34) synthetase
Synonym: YadB
GI: 85674352
Orf: b0144
COG: COG0008
UniProt: P27305
Structures: | 1NZJ | 4A91 |
Alpha Fold Predicted Structure: AF-P27305-F1
Enzyme type: aminoacyl-tRNA synthetase-like
Position of modification - modification: t:34 - gluQ


PDB Structures:


1NZJ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame products of unknown function, we have determined the structure of YadB at 1.5A using molecular replacement. The YadB protein is 298 amino acid residues long and displays 34% sequence identity with E.coli glutamyl-tRNA synthetase (GluRS). It is much shorter than GluRS, which contains 468 residues, and lacks the complete domain interacting with the tRNA anticodon loop. As E.coli GluRS, YadB possesses a Zn2+ located in the putative tRNA acceptor stem-binding domain. The YadB cluster uses cysteine residues as the first three zinc ligands, but has a weaker tyrosine ligand at the fourth position. It shares with canonical amino acid RNA synthetases a major functional feature, namely activation of the amino acid (here glutamate). It differs, however, from GluRSs by the fact that the activation step is tRNA-independent and that it does not catalyze attachment of the activated glutamate to E.coli tRNAGlu, but to another, as yet unknown tRNA. These results suggest thus a novel function, distinct from that of GluRSs, for the yadB gene family.

Download RCSB-PDB Structures:

Pdb Files   1NZJ.pdb   4A91.pdb  
Pdbx/mmCIF Files   1NZJ.cif   4A91.cif  


Protein sequence:

MTDTQYIGRFAPSPSGELHFGSLIAALGSYLQARARQGRWLVRIEDIDPPREVPGAAETILRQLEHYGLHWDGDVLWQSQRHDAYREALAWLHEQGLSYYCTCTRARIQSIGGIYDGHCRVLHHGPDNAAVRIRQQHPVTQFTDQLRGIIHADEKLAREDFIIHRRDGLFAYNLAVVVDDHFQGVTEIVRGADLIEPTVRQISLYQLFGWKVPDYIHLPLALNPQGAKLSKQNHAPALPKGDPRPVLIAALQFLGQQAEAHWQDFSVEQILQSAVKNWRLTAVPESAIVNSTFSNASC

Comments:

The aminoacylation reaction occurs on one of the two free hydroxyl group of Q-base attached to the wobble position 34 of tRNAAsp. The glutamic acid is activated by the formation of an adenylate derivative (Glu-AMP) through a reaction with ATP.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Q:gluQ RNA tRNA 34 GUC GUC tRNAAspGUC wobble - position Prokaryotic Cytosol

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P27305-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P27305-F1.cif  
DSSP Secondary Structures   P27305.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A truncated aminoacyl-tRNA synthetase modifies RNA. Salazar JC, Ambrogelly A, Crain PF, McCloskey JA, Soll D Proc Natl Acad Sci U S A [details] 15096612 -
The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity. Campanacci V, Dubois DY, Becker HD, Kern D, Spinelli S, Valencia C, Pagot F, Salomoni A, Grisel S, Vincentelli R, Bignon C, Lapointe J, Giege R, Cambillau C J Mol Biol [details] 15003446 -
Glu-Q-tRNA(Asp) synthetase coded by the yadB gene, a new paralog of aminoacyl-tRNA synthetase that glutamylates tRNA(Asp) anticodon. Blaise M, Becker HD, Lapointe J, Cambillau C, Giege R, Kern D Biochimie [details] 16164993 -
An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp. Dubois DY, Blaise M, Becker HD, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D Proc Natl Acad Sci U S A [details] 15096594 -
A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon. Blaise M, Becker HD, Keith G, Cambillau C, Lapointe J, Giege R, Kern D Nucleic Acids Res [details] 15150343 -
Crystal structure of glutamyl-queuosine tRNAAsp synthetase complexed with L-glutamate: structural elements mediating tRNA-independent activation of glutamate and glutamylation of tRNAAsp anticodon. Blaise M, Olieric V, Sauter C, Lorber B, Roy B, Karmakar S, Banerjee R, Becker HD, Kern D J Mol Biol [details] 18602926 -

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