Modomics - A Database of RNA Modifications

ID Card:

Full name: Kinase-associated endopeptidase 1
Synonym: YKR038C
GI: 37362674
COG: COG0533
UniProt: P36132
Alpha Fold Predicted Structure: AF-P36132-F1
Complex: EKC/KEOPS
Enzyme type: endopeptidase predicted
Position of modification - modification: t:37 - t6A



Protein sequence:

MVNLNTIPPKNGRDYYIALGLEGSANKLGVGIVKHPLLPKHANSDLSYDCEAEMLSNIRDTYVTPPGEGFLPRDTARHHRNWCIRLIKQALAEADIKSPTLDIDVICFTKGPGMGAPLHSVVIAARTCSLLWDVPLVGVNHCIGHIEMGREITKAQNPVVLYVSGGNTQVIAYSEKRYRIFGETLDIAIGNCLDRFARTLKIPNEPSPGYNIEQLAKKAPHKENLVELPYTVKGMDLSMSGILASIDLLAKDLFKGNKKNKILFDKTTGEQKVTVEDLCYSLQENLFAMLVEITERAMAHVNSNQVLIVGGVGCNVRLQEMMAQMCKDRANGQVHATDNRFCIDNGVMIAQAGLLEYRMGGIVKDFSETVVTQKFRTDEVYAAWRD

Comments:

Cytoplasmic Kae1 (Kinase-Associated Endopeptidase 1) is the ortholog of bacterial TsaD (YgjD) and the paralog of mitochondrial Qri7. It is an iron metalloprotein. Together with other proteins of the so-called EKC/KEOPS complex (Bud32, Pcc1 and Cgi121), ATP, threonine and bicarbonate as cofactors, they catalyze the in vivo formation of t6A (threonyl-carbamoylation, probably a processive type of reaction) at position 37 of all eukaryotic tRNA decoding ANN codons (ile, Met, Thr, Lys, Asn, Arg and Ser). However the detailed stepwise mechanism of t6A formation is still not known (March 2012).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P36132-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P36132-F1.cif  
DSSP Secondary Structures   P36132.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R EMBO J [details] 21183954 -
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V EMBO J [details] 21285948 -
Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Daugeron MC, Lenstra TL, Frizzarin M, El Yacoubi B, Liu X, Baudin-Baillieu A, Lijnzaad P, Decourty L, Saveanu C, Jacquier A, Holstege FC, de Crecy-Lagard V, van Tilbeurgh H, Libri D Nucleic Acids Res [details] 21459853 -

Links:

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