Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA threonylcarbamoyladenosine biosynthesis protein SUA5
GI: 417826
Orf: G1660
COG: COG0009
UniProt: P32579
Alpha Fold Predicted Structure: AF-P32579-F1
Complex: EKC/KEOPS
Enzyme type: threonylcarbamoyladenosine synthetase
Position of modification - modification: t:37 - t6A



Protein sequence:

MYLGRHFLAMTSKALFDTKILKVNPLSIIFSPDAHIDGSLPTITDPETEAALVEAARIIRDTDETVAFPTETVYGLGGSALNDNSVLSIYRAKNRPSDNPLITHVSSIDQLNRKVFNQPHLSGTSLFDNIPSIYRPLISSLWPGPLTILLPVPSSEHSALSKLTTADQPTFAVRIPANPVARALIALSDTPIAAPSANASTRPSPTLASHVYHDLKDKIPIILDGGACKVGVESTVVDGLCNPPTLLRPGGFTYEEIVKLGGEAWSLCKVENKKTVEKGEKVRTPGMKYRHYSPSAKVVLLVPHCEGDGILKGVDRMERLKRLIETELKANSNIKKIAILTSLKLRDSDLQSKIFNEPDFSSKTFIIERLGQSGEEIQTNLFAALRKVDENDKVDLIFVEGINEEGEGLAVMNRLRKAAANNCIQF

Comments:

Sua5 is required for the formation of threonylcarbamoyl group on the adenosine at position 37(t6A37) in almost all tRNAs decoding ANN codons ( Pichard-Kostuch et al. 2018). It likely catalyzes the condensation of L-threonine bicarbonate (HCO-3) and ATP to give threonylcarbamoyl-AMP (TC-AMP). KEOPS/EKC complex is a tRNA modification complex involved in the biosynthesis of N6-threonylcarbamoyl adenosine (t6) ( Wan et al. 2017). In arachaea and eukaryotes, KEOPS/EKC is composed of OSGEP/Kae1, PRPK/Bud32, TPRKB/Cgi121, and LAGE3/PCC1.Fungi contains an additional subbunit, Gon7, whose orthologues in other species, if present, remain unidentified. Together with Sua5, they catalyze the in vivo formation of t6. Structurally,Sua5 displays a YrdC-like domain between A50 and G250. The yrdC-like domain is typically an ~185-residue module which can be found in stand-alone form ( YrdC-like) , or in association with other domains such as the acylphosphatase-like domain which catalyzes the hydrolysis of various acyl phosphate carboxyl-phosphate bonds such as carbamyl phosphate, succinyl phosphate, 1,3-diphosphoglycerate, etc ( YrdC-like).The yrdC-like domain features a large concave surface on one side that exhibits a positive electrostatic potential. The dimension of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that it may be a nucleic acid binding domain.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:t6A RNA tRNA 37 tRNAANN anticodon-loop Cytoplasm, Nucleus 19287007   
A:t6A RNA tRNA 37 GUU GUU tRNAAsnGUU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 IAU IAU tRNAIleIAU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 PAP PAP tRNAIlePAP Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 GAU GAU tRNAIleGAU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 CAU CAU tRNAMetCAU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 CAU CAU tRNAMetCAU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 UCU UCU tRNAArgUCU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 NCU NCU tRNAArgNCU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 IGU IGU tRNAThrIGU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 CUU CUU tRNALysCUU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 3UU 3UU tRNALys3UU Anticodon-loop Cytoplasm
A:t6A RNA tRNA 37 $UU $UU tRNALys$UU Anticodon-loop Cytoplasm

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P32579-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P32579-F1.cif  
DSSP Secondary Structures   P32579.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae. Na JG, Pinto I, Hampsey M Genetics [details] 1325384 -
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 -
The Sua5 protein is essential for normal translational regulation in yeast. Lin CA, Ellis SR, True HL Mol Cell Biol [details] 19884342 -