Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA-processing protein 8
Synonym: YDR083W
GI: 398365487
Orf: D4461
COG: COG0500
UniProt: P38961
Structures: | 2ZFU |
Alpha Fold Predicted Structure: AF-P38961-F1
Enzyme type: methyltransferase
Position of modification - modification: l:645(571) - m1A


PDB Structures:


2ZFU

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Intracellular energy balance is important for cell survival. In eukaryotic cells, the most energy-consuming process is ribosome biosynthesis, which adapts to changes in intracellular energy status. However, the mechanism that links energy status and ribosome biosynthesis is largely unknown. Here, we describe eNoSC, a protein complex that senses energy status and controls rRNA transcription. eNoSC contains Nucleomethylin, which binds histone H3 dimethylated Lys9 in the rDNA locus, in a complex with SIRT1 and SUV39H1. Both SIRT1 and SUV39H1 are required for energy-dependent transcriptional repression, suggesting that a change in the NAD(+)/NADH ratio induced by reduction of energy status could activate SIRT1, leading to deacetylation of histone H3 and dimethylation at Lys9 by SUV39H1, thus establishing silent chromatin in the rDNA locus. Furthermore, eNoSC promotes restoration of energy balance by limiting rRNA transcription, thus protecting cells from energy deprivation-dependent apoptosis. These findings provide key insight into the mechanisms of energy homeostasis in cells.

Download RCSB-PDB Structures:

Pdb Files   2ZFU.pdb  
Pdbx/mmCIF Files   2ZFU.cif  


Protein sequence:

MALFNVEGWSIKTKTVAFDNKTNKSSKDKKKNNRKNGKLTREQKLKEETEAELKEQVEDIPSEGSVAKDIPKKNQEKSDQNETSKKRKHDEEAPLMQVKENIEKPTKKQLTPLQQKMMAKLTGSRFRWINEQLYTISSDEALKLIKEQPQLFDEYHDGFRSQVQAWPENPVDVFVDQIRYRCMKPVNAPGGLPGLKDSKEIVIADMGCGEAQLALEINNFFKNYNKKAKKYLKRRHKVHSFDLKKANERITVADIRNVPLPDESCTIVVFCLALMGTNFLDFIKEAYRILAPRGELWIAEIKSRFSDGKGNEFVDALKLMGFFHKKTFDENKMFTRFEFFKPPAEIIEERRQKLERRQKFIEVETEKEELEKKRRKIAEGKWLLKPCIYKRR

Comments:

Required for efficient pre-35S rRNA cleavage at site A2. Remains associated to the resulting 27S product. Also involved in telomere length regulation and maintenance. This nucleolar Rossmann-fold like protein is highly conserved in eukaryotes and catalyses the N1-methylation of A645 in helix 25.1 of 25S rRNA. However the methylation function is independent of the A2-cleavage reaction, attesting that Rrp8p has a dual function. The introduction of a methyl group at N1 of adenosine, introduces a positive charge to the nucleoside.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m1A rRNA (r) LSU-L/25S/eukaryotic cytosol 645 LSU-L 25S Nucleolus

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P38961-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P38961-F1.cif  
DSSP Secondary Structures   P38961.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Rrp8p is a yeast nucleolar protein functionally linked to Gar1p and involved in pre-rRNA cleavage at site A2. Bousquet-Antonelli C, Vanrobays E, Gelugne JP, Caizergues-Ferrer M, Henry Y... RNA [details] 10864042 -
Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Peifer C, Sharma S, Watzinger P, Lamberth S, Kotter P, Entian KD... Nucleic Acids Res [details] 23180764 -

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