Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (uracil-5-)-methyltransferase
Synonym: Nud1, Rnc1
GI: 110825750
Orf: YKR056W
COG: COG2265
UniProt: P33753
Alpha Fold Predicted Structure: AF-P33753-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m5U



Protein sequence:

MYEQFEFSFFFFENSDNKVKYKAHLISSIKRWSIITCMRCFWTVQKSIFKARFFACRNFVKKHNYKLISTMTGSTEMVPPTMKHTVDNKRLSSPLTDSGNRRTKKPKLRKYKAKKVETTSPMGVLEFEVNDLLKSQNLSREQVLNDVTSILNDKSSTDGPIVLQYHREVKNVKVLEITSNGNGLALIDNPVETEKKQVVIIPFGLPGDVVNIKVFKTHPYYVESDLLDVVEKSPMRRDDLIRDKYFGKSSGSQLEFLTYDDQLELKRKTIMNAYKFFAPRLVAEKLLPPFDTTVASPLQFGYRTKITPHFDMPKRKQKELSVRPPLGFGQKGRPQWRKDTLDIGGHGSILDIDECVLATEVLNKGLTNERRKFEQEFKNYKKGATILLRENTTILDPSKPTLEQLTEEASRDENGDISYVEVEDKKNNVRLAKTCVTNPRQIVTEYVDGYTFNFSAGEFFQNNNSILPIVTKYVRDNLQAPAKGDDNKTKFLVDAYCGSGLFSICSSKGVDKVIGVEISADSVSFAEKNAKANGVENCRFIVGKAEKLFESIDTPSENTSVILDPPRKGCDELFLKQLAAYNPAKIIYISCNVHSQARDVEYFLKETENGSAHQIESIRGFDFFPQTHHVESVCIMKRI

Comments:

S-Adenosyl methionine (SAM or AdoMet) consists of an adenosyl cation attached to the sulfur methionine. It is synthesized from ATP and methionine by S-Adenosylmethionine synthetase enzyme through the reaction of ATP with L-methionine and water forming as catalytical product S-adenosyl-L-methionine. SAM is a common cosubstrate involved in several reactions, among which methyl group transfers. Trm2 is a site-specific enzymes catalyzing the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA ( Nordlund et al. 2000). It contains 1 TRAM) domain, a typically 60-70 residue-long module that can be found alone or in association with other domains, such as the RNA methylase domain. TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:m5U RNA tRNA 54 IGC IGC tRNAAlaIGC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 ACU ACU tRNAArgACU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 ICG ICG tRNAArgICG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GUU GUU tRNAAsnGUU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GUC GUC tRNAAspGUC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GCA GCA tRNACysGCA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CUC CUC tRNAGluCUC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GCC GCC tRNAGlyGCC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 {CC {CC tRNAGly{CC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GUG GUG tRNAHisGUG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 IAU IAU tRNAIleIAU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAU UAU tRNAIleUAU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAG UAG tRNALeuUAG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CAA CAA tRNALeuCAA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAA UAA tRNALeuUAA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CUU CUU tRNALysCUU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 SUU SUU tRNALysSUU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CAU CAU tRNAMetCAU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GAA GAA tRNAPheGAA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UGG UGG tRNAProUGG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CGA CGA tRNASerCGA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UGA UGA tRNASerUGA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 IGA IGA tRNASerIGA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 IGU IGU tRNAThrIGU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CCA CCA tRNATrpCCA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CAC CAC tRNAValCAC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAC UAC tRNAValUAC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 IAC IAC tRNAValIAC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UCU UCU tRNAArgUCU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 ACG ACG tRNAArgACG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UCC UCC tRNAGlyUCC TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GUG GUG tRNAHisGUG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GAU GAU tRNAIleGAU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAA UAA tRNALeuUAA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UUU UUU tRNALysUUU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 CAU CAU tRNAMetCAU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UGG UGG tRNAProUGG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GCU GCU tRNASerGCU TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UGA UGA tRNASerUGA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UAG UAG tRNAThrUAG TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 UCA UCA tRNATrpUCA TΨC-loop Maybe Nucleus 10864043   
U:m5U RNA tRNA 54 GUA GUA tRNATyrGUA TΨC-loop Maybe Nucleus 10864043   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P33753-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P33753-F1.cif  
DSSP Secondary Structures   P33753.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae. Nordlund ME, Johansson JO, von Pawel-Rammingen U, Bystrom AS RNA [details] 10864043 -