Modomics - A Database of RNA Modifications

ID Card:

Full name: Methyltransferase type 12
Synonym: Cthe_2767
GI: 125975249
COG: COG2227
UniProt: A3DJ37
Structures: | 3JWI | 3JWG |
Alpha Fold Predicted Structure: AF-A3DJ37-F1
Enzyme type: methyltransferase
Position of modification - modification: undefined RNA: 3' end Nm


PDB Structures:


3JWI

Structure Description:

Title: Crystal structure analysis of the methyltransferase domain of bacterial-CtHen1-C
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 1.9
R value free: 0.234
R value observed:
R value work: 0.218

Abstract of the PDB Structure's related Publication:

Small RNAs of approximately 20-30 nt have diverse and important biological roles in eukaryotic organisms. After being generated by Dicer or Piwi proteins, all small RNAs in plants and a subset of small RNAs in animals are further modified at their 3'-terminal nucleotides via 2'-O-methylation, carried out by the S-adenosylmethionine-dependent methyltransferase (MTase) Hen1. Methylation at the 3' terminus is vital for biological functions of these small RNAs. Here, we report four crystal structures of the MTase domain of a bacterial homolog of Hen1 from Clostridium thermocellum and Anabaena variabilis, which are enzymatically indistinguishable from the eukaryotic Hen1 in their ability to methylate small single-stranded RNAs. The structures reveal that, in addition to the core fold of the MTase domain shared by other RNA and DNA MTases, the MTase domain of Hen1 possesses a motif and a domain that are highly conserved and are unique to Hen1. The unique motif and domain are likely to be involved in RNA substrate recognition and catalysis. The structures allowed us to construct a docking model of an RNA substrate bound to the MTase domain of bacterial Hen1, which is likely similar to that of the eukaryotic counterpart. The model, supported by mutational studies, provides insight into RNA substrate specificity and catalytic mechanism of Hen1.

Download RCSB-PDB Structures:

Pdb Files   3JWG.pdb   3JWI.pdb  
Pdbx/mmCIF Files   3JWG.cif   3JWI.cif  


Protein sequence:

MILTITYTQPPATDLGYLLHKNPSRPQTFELNHGKAHIFYPEATSERCTVALLLDIDPIDLARGKKGSSGEGGLFDYVNDRPYVSSSFMSVAISRVFGTAMSGKCKEKPELAAIKLPLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSRYYTVSLEGEVRVRDLLNHIYVLIPVLDSEKHYWVGEDEIDKLFQHGEGWLVDHPEKELITGRYLIRKKRLVNQALKRLLEASDVVDDENEDDEPLKNEETEKKLNLNQQRLGTVVAVLKSVNAKKVIDLGCGEGNLLSLLLKDKSFEQITGVDVSYSVLERAKDRLKIDRLPEMQRKRISLFQSSLVYRDKRFSGYDAATVIEVIEHLDENRLQAFEKVLFEFTRPQTVIVSTPNKEYNFHYQNLFEGNLRHRDHRFEWTRKEFETWAVKVAEKYGYSVRFLQIGEIDDEFGSPTQMGVFTL

Comments:

Homodimer. Manganese dependent. Part of RNA repair system. Methylates 3' end of broken RNAs. Unlike eukaryotic Hen1 involved in RNA interference, the bacterial Hen1 is part of an RNA repair and modification system. Animal homologue of Hen1 modifies piRNA and is important for germ cell development.





Alpha Fold Predicted Structure:




Parsing response... [440006/440006]


Clear Selection and Reset Camera

Protein sequence:

M I L T I T Y T Q P P A T D L G Y L L H K N P S R P Q T F E L N H G K A H I F Y P E A T S E R C T V A L L L D I D P I D L A R G K K G S S G E G G L F D Y V N D R P Y V S S S F M S V A I S R V F G T A M S G K C K E K P E L A A I K L P L K A K I M M L P C K G G E E I I Y R L F E P L G Y K V D V E G Y M L D E K F P E W G K S R Y Y T V S L E G E V R V R D L L N H I Y V L I P V L D S E K H Y W V G E D E I D K L F Q H G E G W L V D H P E K E L I T G R Y L I R K K R L V N Q A L K R L L E A S D V V D D E N E D D E P L K N E E T E K K L N L N Q Q R L G T V V A V L K S V N A K K V I D L G C G E G N L L S L L L K D K S F E Q I T G V D V S Y S V L E R A K D R L K I D R L P E M Q R K R I S L F Q S S L V Y R D K R F S G Y D A A T V I E V I E H L D E N R L Q A F E K V L F E F T R P Q T V I V S T P N K E Y N F H Y Q N L F E G N L R H R D H R F E W T R K E F E T W A V K V A E K Y G Y S V R F L Q I G E I D D E F G S P T Q M G V F T L
50100150200250300350400450SequenceGHITBSN

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-A3DJ37-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-A3DJ37-F1.cif  
DSSP Secondary Structures   A3DJ37.dssp  





Publications:

Links:

_PubMed_