Modomics - A Database of RNA Modifications

ID Card:

Full name: Alpha-tubulin suppressor 1
Synonym: ATS1
GI: 330443378
Orf: FUN28, YAL006
COG: COG5184
UniProt: P31386
Structures: | 4D4Q | 4D4O | 4D4P |
Alpha Fold Predicted Structure: AF-P31386-F1


PDB Structures:


4D4Q

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The small, highly conserved Kti11 alias Dph3 protein encoded by the Kluyveromyces lactis killer toxin insensitive gene KTI11/DPH3 is involved in the diphthamide modification of eukaryotic elongation factor 2 and, together with Kti13, in Elongator-dependent tRNA wobble base modifications, thereby affecting the speed and accuracy of protein biosynthesis through two distinct mechanisms. We have solved the crystal structures of Saccharomyces cerevisiae Kti13 and the Kti11/Kti13 heterodimer at 2.4 and 2.9 Å resolution, respectively, and validated interacting residues through mutational analysis in vitro and in vivo. We show that metal coordination by Kti11 and its heterodimerization with Kti13 are essential for both translational control mechanisms. Our structural and functional analyses identify Kti13 as an additional component of the diphthamide modification pathway and provide insight into the molecular mechanisms that allow the Kti11/Kti13 heterodimer to coregulate two consecutive steps in ribosomal protein synthesis.

Download RCSB-PDB Structures:

Pdb Files   4D4O.pdb   4D4P.pdb   4D4Q.pdb  
Pdbx/mmCIF Files   4D4O.cif   4D4P.cif   4D4Q.cif  


Protein sequence:

MSCVYAFGSNGQRQLGLGHDEDMDTPQRSVPGDDGAIVRKIACGGNHSVMLTNDGNLVGCGDNRRGELDSAQALRQVHDWRPVEVPAPVVDVACGWDTTVIVDADGRVWQRGGGCYEFTQQHVPLNSNDERIAVYGCFQNFVVVQGTRVYGWGSNTKCQLQEPKSRSLKEPVLVYDTGSVAVDYVAMGKDFMVIVDEGGRIVHASGRLPTGFELKQQQKRHNLVVLCMWTSIHLWNARLNTVESFGRGTHSQLFPQERLDFPIVGVATGSEHGILTTANQEGKSHCYNVYCWGWGEHGNCGPQKGSQPGLQLVGQYSGKPRVFGGCATTWIVL

Comments:

One of the many protein cofactors required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA. The enzyme that catalyzes this reaction is still unknown (2012).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S C V Y A F G S N G Q R Q L G L G H D E D M D T P Q R S V P G D D G A I V R K I A C G G N H S V M L T N D G N L V G C G D N R R G E L D S A Q A L R Q V H D W R P V E V P A P V V D V A C G W D T T V I V D A D G R V W Q R G G G C Y E F T Q Q H V P L N S N D E R I A V Y G C F Q N F V V V Q G T R V Y G W G S N T K C Q L Q E P K S R S L K E P V L V Y D T G S V A V D Y V A M G K D F M V I V D E G G R I V H A S G R L P T G F E L K Q Q Q K R H N L V V L C M W T S I H L W N A R L N T V E S F G R G T H S Q L F P Q E R L D F P I V G V A T G S E H G I L T T A N Q E G K S H C Y N V Y C W G W G E H G N C G P Q K G S Q P G L Q L V G Q Y S G K P R V F G G C A T T W I 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-P31386-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P31386-F1.cif  
DSSP Secondary Structures   P31386.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. Huang B, Lu J, Bystrom AS RNA [details] 18755837 -
An early step in wobble uridine tRNA modification requires the Elongator complex. Huang B, Johansson MJ, Bystrom AS RNA [details] 15769872 -
Structure of the Kti11/Kti13 Heterodimer and Its Double Role in Modifications of tRNA and Eukaryotic Elongation Factor 2. Glatt S, Zabel R, Vonkova I, Kumar A, Netz DJ, Pierik AJ, Rybin V, Lill R, Gavin A, Balbach J, Breunig KD, Muller CW... Structure [details] 25543256 -

Links:

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