Modomics - A Database of RNA Modifications

ID Card:

Full name: t(6)A37 threonylcarbamoyladenosine biosynthesis protein QRI7
Synonym: OSGEPL, YDL104C
GI: 6320099
Orf: D2366
COG: COG0533
UniProt: P43122
Structures: | 3WUH | 4K25 |
Alpha Fold Predicted Structure: AF-P43122-F1
Enzyme type: threonylcarbamoyltransferase
Position of modification - modification: t:37 - t6A


PDB Structures:


3WUH

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

N(6)-Threonylcarbamoyladenosine (t(6)A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t(6)A biosynthesis. In t(6)A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t(6)A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.

Download RCSB-PDB Structures:

Pdb Files   3WUH.pdb   4K25.pdb  
Pdbx/mmCIF Files   3WUH.cif   4K25.cif  


Protein sequence:

MISIKGTGRFLLDNYRIWQRRAFNRPIQLRKGYKVLAIETSCDDTCVSVLDRFSKSAAPNVLANLKDTLDSIDEGGIIPTKAHIHHQARIGPLTERALIESNAREGIDLICVTRGPGMPGSLSGGLDFAKGLAVAWNKPLIGVHHMLGHLLIPRMGTNGKVPQFPFVSLLVSGGHTTFVLSRAIDDHEILCDTIDIAVGDSLDKCGRELGFKGTMIAREMEKFINQDINDQDFALKLEMPSPLKNSASKRNMLSFSFSAFITALRTNLTKLGKTEIQELPEREIRSIAYQVQESVFDHIINKLKHVLKSQPEKFKNVREFVCSGGVSSNQRLRTKLETELGTLNSTSFFNFYYPPMDLCSDNSIMIGWAGIEIWESLRLVSDLDICPIRQWPLNDLLSVDGWRTDQL

Comments:

This protein is the mitochondrial paralog of cytoplasmic Kae1 and ortholog of bacterial TsaD (YgjD). Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in mitochondrial tRNAs that read codons beginning with adenine. Qri7 alone is sufficient to catalyze the transfer of the threonyl-carbamoyl group to adenine 37 of tRNA, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P43122-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P43122-F1.cif  
DSSP Secondary Structures   P43122.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V EMBO J [details] 21285948 -
Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Oberto J, Breuil N, Hecker A, Farina F, Brochier-Armanet C, Culetto E, Forterre P Nucleic Acids Res [details] 19578062 -
Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O... Acta Crystallogr F Struct Biol Commun [details] 25084372 -

Links:

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