Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-specific cytidine deaminase
Synonym: MK0935
GI: 238537840
COG: COG2131
UniProt: Q8TWU6
Structures: | 3G8Q |
Alpha Fold Predicted Structure: AF-Q8TWU6-F1
Enzyme type: deaminase
Position of modification - modification: t:8 - U


PDB Structures:


3G8Q

Structure Description:

Title: A cytidine deaminase edits C-to-U in transfer RNAs in archaea
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 2.4
R value free: 0.265
R value observed: 0.205
R value work: 0.202

Abstract of the PDB Structure's related Publication:

All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.

Download RCSB-PDB Structures:

Pdb Files   3G8Q.pdb  
Pdbx/mmCIF Files   3G8Q.cif  


Protein sequence:

MKVSLAGQTVDVKKILNEIPKRTVTAALLEGGEIVAVEEADDEHAERKLVRRHDVEGKVVFVTARPCLYCARELAEAGVAGVVYLGRGRGLGPYYLARSGVEVVEVHPDEPLGYDPVDRLDVLLTFGGNPYLTEEDVAARVYCLLTGRGFDADIAPAPENLSGRVEIMVTRGDPDEAVELLKEELPVFRIRRFLISGEFDRDELRERILEDIEPRILDPFAVRARIARAGAFSSSREAEVFIGDVLTSVGREVNLNDPRTVVTVDVLGPRVSVGVEKR

Comments:

CDAT8 is responsible for C-to-U editing at position 8 in tRNA. It is composed of three domains: an N-terminal cytidine deaminase domain (CDD), a central ferredoxin-like domain (FLD), and a C-terminal THUMP domain. Works as a dimer. In Methanopyrus kandleri, only four tRNAs (tRNAGln UUG, tRNAPro GGG, tRNAPro UGG, and tRNAThr GGU) possess a U8 (T8 in the tRNA gene), whereas the other 30 tRNA genes encode C8. The highly conserved U8 in tRNAs forms a reverse Hoogsteen tertiary base pair with A14 that stabilizes the sharp kink between the acceptor stem and base A9. The C8 must be modified to U in order to support the tertiary interaction with A14, which is present in all 34 tRNAs.





Alpha Fold Predicted Structure:




Parsing response... [254854/254854]


Clear Selection and Reset Camera

Protein sequence:

M K V S L A G Q T V D V K K I L N E I P K R T V T A A L L E G G E I V A V E E A D D E H A E R K L V R R H D V E G K V V F V T A R P C L Y C A R E L A E A G V A G V V Y L G R G R G L G P Y Y L A R S G V E V V E V H P D E P L G Y D P V D R L D V L L T F G G N P Y L T E E D V A A R V Y C L L T G R G F D A D I A P A P E N L S G R V E I M V T R G D P D E A V E L L K E E L P V F R I R R F L I S G E F D R D E L R E R I L E D I E P R I L D P F A V R A R I A R A G A F S S S R E A E V F I G D V L T S V G R E V N L N D P R T V V T V D V L G P R V S V G V E K R
20406080100120140160180200220240260SequenceGHITBSN

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-Q8TWU6-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8TWU6-F1.cif  
DSSP Secondary Structures   Q8TWU6.dssp  





Publications:

Links:

_Wikipedia_-_RNA_editing_
_Wikipedia_-_Deamination_