Modomics - A Database of RNA Modifications

ID Card:

Full name: Serine/threonine-protein kinase BUD32
Synonym: PRPK, LDB14, YGR262c
GI: 6321701
COG: COG3642
UniProt: P53323
Structures: | 4WW5 | 4WW7 | 4WW9 | 4WWA |
Alpha Fold Predicted Structure: AF-P53323-F1
Complex: EKC/KEOPS
Enzyme type: kinase
Position of modification - modification: t:37 - t6A


PDB Structures:


4WW5

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The yeast KEOPS protein complex comprising Kae1, Bud32, Cgi121, Pcc1 and Gon7 is responsible for the essential tRNA threonylcarbamoyladenosine (t(6)A) modification. Deletion of genes coding for the KEOPS subunits also affects telomere elongation and transcriptional regulation. In the present work, the crystal structure of Bud32/Cgi121 in complex with ADP revealed that ADP is bound in the catalytic site of Bud32 in a canonical manner characteristic of Protein Kinase A (PKA) family proteins. We found that Gon7 forms a stable heterodimer with Pcc1 and report the crystal structure of the Pcc1-Gon7 heterodimer. Gon7 interacts with the same Pcc1 region engaged in the archaeal Pcc1 homodimer. We further show that yeast KEOPS, unlike its archaeal counterpart, exists as a heteropentamer in which Gon7, Pcc1, Kae1, Bud32 and Cgi121 also adopt a linear arrangement. We constructed a model of yeast KEOPS that provides structural insight into the role of Gon7. The model also revealed the presence of a highly positively charged crater surrounding the entrance of Kae1 that likely binds tRNA.

Download RCSB-PDB Structures:

Pdb Files   4WW5.pdb   4WW7.pdb   4WW9.pdb   4WWA.pdb  
Pdbx/mmCIF Files   4WW5.cif   4WW7.cif   4WW9.cif   4WWA.cif  


Protein sequence:

MTQEFIDKVSSYLTPDVDIAPISQGAEAIVFTTTTHPYLPRAKDSHQKYIIKYRPPKRYRHPQIDQALTKHRTLNESRLLAKLYLIPGLCVPQLIACDPYNGFIWLEFLGEDLPGGHGFSNLKNFLWMHDQDPYSDLVATTLRKVGRQIGLLHWNDYCHGDLTSSNIVLVRDGARWTPHLIDFGLGSVSNLVEDKGVDLYVLERAILSTHSKHAEKYNAWIMEGFEEVYREQGAKGAKKLKEVTKRFEEVRLRGRKRSMLG

Comments:

Member of the protein kinase superfamily Bud32 is conserved in all eukaryotic and archaeal organisms. It is absent in bacteria. Bud32 forms part of the KEOPS (kinase Endopeptidase and other proteins of small size) complex together with other subunits. KEOPS works generating t6A, an essential post-transcriptional modification, that is is present in tRNAs. This modification is present in position A37 and binds to ANN codons. This modification ensures translation fidelity. It is a RIO-type kinase (PRPK), a p53-related protein kinase in human. At variance with most archaeal Bud32, the S. cerevisiae Bud32 is not fused to SceKae1




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:t6A RNA tRNA 37 AGC AGC tRNAThrAGT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 AGG AGG tRNASerGCT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 CCT CCT tRNAArgCCT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 TCT TCT tRNAArgTCT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 GTT GTT tRNAAsnGTT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 CTT CTT tRNALysCTT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 TTT TTT tRNALysTTT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 AAT AAT tRNAIleAAT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 TAT TAT tRNAIleTAT anticodon-loop Nucleoplasm 19143597   
A:t6A RNA tRNA 37 CAT CAT tRNAMetCAT anticodon-loop Nucleoplasm 19143597   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P53323-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P53323-F1.cif  
DSSP Secondary Structures   P53323.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 -

Links:

_PubMed_