Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA N6-threonylcarbamoyladenosine(37) synthesis protein
Synonym: RimN, yrdC
GI: 2851671
COG: COG0009
UniProt: P45748
Structures: | 1HRU | 2MX1 |
Alpha Fold Predicted Structure: AF-P45748-F1
Enzyme type: threonylcarbamoyladenosine synthetase
Position of modification - modification: t:37 - t6A


PDB Structures:


1HRU

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The yrdC family of genes codes for proteins that occur both independently and as a domain in proteins that have been implicated in regulation. An example for the latter case is the sua5 gene from yeast. SuaS was identified as a suppressor of a translation initiation defect in cytochrome c and is required for normal growth in yeast (Na JG, Pinto I, Hampsey M, 1992, Genetics 11:791-801). However, the function of the Sua5 protein remains unknown; Sua5 could act either at the transcriptional or the posttranscriptional levels to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring this domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 A. YrdC adopts a new fold with no obvious similarity to those of other proteins with known three-dimensional (3D) structure. The protein features a large concave surface on one side that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that YrdC may be a nucleic acid binding protein. An investigation of YrdC's binding affinities for single- and double-stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC binds preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique sequences can yield novel folds and functional insights.

Download RCSB-PDB Structures:

Pdb Files   1HRU.pdb   2MX1.pdb  
Pdbx/mmCIF Files   1HRU.cif   2MX1.cif  


Protein sequence:

MNNNLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKPYIDDTMLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVVPGETGGRLNPSEIRDALTGELFRQG

Comments:

TsaC, the bacterial ortholog of eukaryal and archaeal Sua5, is an ATPase (produces AMP) that binds A37-containing tRNA, but not threonine. Together with 3 other proteins (TsaD=YgjD, TsaB=YeaZ and TsaE=YjeE), ATP, threonine and bicarbonate as cofactors, they catalyze the in vitro formation of t6A (threonyl-carbamoylation) at position 37 of all bacterial tRNA decoding ANN codons (ile, Met, Thr, Lys, Asn, Ser and Arg). However the detailed stepwise mechanism of t6A formation is still not known (March 2012).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P45748-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P45748-F1.cif  
DSSP Secondary Structures   P45748.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M Protein Sci [details] 11206077 -
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V Nucleic Acids Res [details] 19287007 -
YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. Harris KA, Jones V, Bilbille Y, Swairjo MA, Agris PF RNA [details] 21775474 -
Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D J Biol Chem [details] 22378793 -

Links:

_EcoCyc_