Modomics - A Database of RNA Modifications

ID Card:

Full name:	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Synonym:	MJ1130
GI:	15669317
COG:	COG0533
UniProt:	Q58530
Structures:	\| 3ENH \| 3EN9 \| 2VWB \| 5JMV \|
Alpha Fold Predicted Structure:	AF-Q58530-F1
Complex:	EKC/KEOPS
Enzyme type:	endopeptidase/kinase predicted
Position of modification - modification:	t:37 - t6A

PDB Structures:

3ENH

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The EKC/KEOPS yeast complex is involved in telomere maintenance and transcription. The Bud32p and kinase-associated endopeptidase 1 (Kaelp) components of the complex are totally conserved in eukarya and archaea. Their genes are fused in several archaeal genomes, suggesting that they physically interact. We report here the structure of the Methanocaldococcus jannaschii Kae1/Bud32 fusion protein MJ1130. Kae1 is an iron protein with an ASKHA fold and Bud32 is an atypical small RIO-type kinase. The structure MJ1130 suggests that association with Kae1 maintains the Bud32 kinase in an inactive state. We indeed show that yeast Kae1p represses the kinase activity of yeast Bud32p. Extensive conserved interactions between MjKae1 and MjBud32 suggest that Kae1p and Bud32p directly interact in both yeast and archaea. Mutations that disrupt the Kae1p/Bud32p interaction in the context of the yeast complex have dramatic effects in vivo and in vitro, similar to those observed with deletion mutations of the respective components. Direct interaction between Kae1p and Bud32p in yeast is required both for the transcription and the telomere homeostasis function of EKC/KEOPS.

Download RCSB-PDB Structures:

Pdb Files	2VWB.pdb 3EN9.pdb 3ENH.pdb 5JMV.pdb
Pdbx/mmCIF Files	2VWB.cif 3EN9.cif 3ENH.cif 5JMV.cif

Protein sequence:

MICLGLEGTAEKTGVGIVTSDGEVLFNKTIMYKPPKQGINPREAADHHAETFPKLIKEAFEVVDKNEIDL
IAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVS
KKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAY
DAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKE
FCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWIKEIKGKKRKIPEHLIGKGAEADIKRD
SYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKL
AKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDEDKAVDLIVFKKA
VLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERRARYVE

Comments:

Archaeal Kae1 (Kinase-Associated Endopeptidase 1) is the ortholog eukaryal Kae1/bacterial TsaD (YgjD) and the paralog of mitochondrial Qri7. In M. jannaschi, as in most archaea, it is fused to Bud32 kinase. This iron metalloprotein Kae1, 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 I C L G L E G T A E K T G V G I V T S D G E V L F N K T I M Y K P P K Q G I N P R E A A D H H A E T F P K L I K E A F E V V D K N E I D L I A F S Q G P G L G P S L R V T A T V A R T L S L T L K K P I I G V N H C I A H I E I G K L T T E A E D P L T L Y V S G G N T Q V I A Y V S K K Y R V F G E T L D I A V G N C L D Q F A R Y V N L P H P G G P Y I E E L A R K G K K L V D L P Y T V K G M D I A F S G L L T A A M R A Y D A G E R L E D I C Y S L Q E Y A F S M L T E I T E R A L A H T N K G E V M L V G G V A A N N R L R E M L K A M C E G Q N V D F Y V P P K E F C G D N G A M I A W L G L L M H K N G R W M S L D E T K I I P N Y R T D M V E V N W I K E I K G K K R K I P E H L I G K G A E A D I K R D S Y L D F D V I I K E R V K K G Y R D E R L D E N I R K S R T A R E A R Y L A L V K D F G I P A P Y I F D V D L D N K R I M M S Y I N G K L A K D V I E D N L D I A Y K I G E I V G K L H K N D V I H N D L T T S N F I F D K D L Y I I D F G L G K I S N L D E D K A V D L I V F K K A V L S T H H E K F D E I W E R F L E G Y K S V Y D R W E I I L E L M K D V E R R A R Y V E

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-Q58530-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-Q58530-F1.cif
DSSP Secondary Structures	Q58530.dssp

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya.	Hecker A, Graille M, Madec E, Gadelle D, Le Cam E, van Tilbergh H, Forterre P	Biochem Soc Trans	[details]	19143597	-
Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.	Mao DY, Neculai D, Downey M, Orlicky S, Haffani YZ, Ceccarelli DF, Ho JS, Szilard RK, Zhang W, Ho CS, Wan L, Fares C, Rumpel S, Kurinov I, Arrowsmith CH, Durocher D, Sicheri F	Mol Cell	[details]	18951093	-
Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex.	Hecker A, Lopreiato R, Graille M, Collinet B, Forterre P, Libri D, van Tilbeurgh H	EMBO J	[details]	19172740	-

Links:

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