Modomics - A Database of RNA Modifications

ID Card:

Full name: putative RNA 5-methyluridine methyltransferase
Synonym: TTHA1280
GI: 55981249
COG: COG1092
UniProt: Q5SIT4
Structures: | 1WXW | 1WXX | 2CWW |
Alpha Fold Predicted Structure: AF-Q5SIT4-F1
Enzyme type: methyltransferase predicted
Position of modification - modification: l:1984(1962) - m5C


PDB Structures:


1WXW

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The Thermus thermophilus hypothetical protein TTHA1280 belongs to a family of predicted S-adenosyl-L-methionine (AdoMet) dependent RNA methyltransferases (MTases) present in many bacterial and archaeal species. Inspection of amino-acid sequence motifs common to class I Rossmann-fold-like MTases suggested a specific role as an RNA 5-methyluridine MTase. Selenomethionine (SeMet) labelled and native versions of the protein were expressed, purified and crystallized. Two crystal forms of the SeMet-labelled apoprotein were obtained: SeMet-ApoI and SeMet-ApoII. Cocrystallization of the native protein with S-adenosyl-L-homocysteine (AdoHcy) yielded a third crystal form, Native-AdoHcy. The SeMet-ApoI structure was solved by the multiple anomalous dispersion method and refined at 2.55 A resolution. The SeMet-ApoII and Native-AdoHcy structures were solved by molecular replacement and refined at 1.80 and 2.60 A, respectively. TTHA1280 formed a homodimer in the crystals and in solution. Each subunit folds into a three-domain structure composed of a small N-terminal PUA domain, a central alpha/beta-domain and a C-terminal Rossmann-fold-like MTase domain. The three domains form an overall clamp-like shape, with the putative active site facing a deep cleft. The architecture of the active site is consistent with specific recognition of uridine and catalysis of methyl transfer to the 5-carbon position. The cleft is suitable in size and charge distribution for binding single-stranded RNA.

Download RCSB-PDB Structures:

Pdb Files   1WXW.pdb   1WXX.pdb   2CWW.pdb  
Pdbx/mmCIF Files   1WXW.cif   1WXX.cif   2CWW.cif  


Protein sequence:

MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL

Comments:

TTHA1280 is E. coli RlmI homologue. Mutant studies show that deltaTTHA1280 strain completely lacks the methyl group on the RNase A digestion product harboring C1962.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M R I Q V N A K G A A R L L S R H L W V F R R D V V S G P E T P G L Y P V Y W G R R F L A L A L Y N P H T D L A V R A Y R F A P A E D P V A A L L E N L A Q A L A R R E A V L R Q D P E G G Y R L V H A E G D L L P G L V V D Y Y A G H A V V Q A T A H A W E G L L P Q V A E A L R P H V Q S V L A K N D A R T R E L E G L P L Y V R P L L G E V P E R V Q V Q E G R V R Y L V D L R A G Q K T G A Y L D Q R E N R L Y M E R F R G E R A L D V F S Y A G G F A L H L A L G F R E V V A V D S S A E A L R R A E E N A R L N G L G N V R V L E A N A F D L L R R L E K E G E R F D L V V L D P P A F A K G K K D V E R A Y R A Y K E V N L R A I K L L K E G G I L A T A S C S H H M T E P L F Y A M V A E A A Q D A H R L L R V V E K R G Q P F D H P V L L N H P E T H Y L K F A V F Q V 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-Q5SIT4-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SIT4-F1.cif  
DSSP Secondary Structures   Q5SIT4.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification and characterization of the Thermus thermophilus 5-methylcytidine (m5C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942. Larsen LH, Rasmussen A, Giessing AM, Jogl G, Kirpekar F... J Biol Chem [details] 22711535 -
Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine. Pioszak AA, Murayama K, Nakagawa N, Ebihara A, Kuramitsu S, Shirouzu M, Yokoyama S... Acta Crystallogr Sect F Struct Biol Cryst Commun [details] 16511182 -