Modomics - A Database of RNA Modifications

ID Card:

Full name: AdoMet-dependent rRNA methyltransferase SPB1
Synonym: YCL54W, YCL431
GI: 6226708
Orf: YCL054W
COG: COG0293
UniProt: P25582
Structures: | 6ELZ | 6EM5 | 6YLX | 7OHR | 7OHV |
Alpha Fold Predicted Structure: AF-P25582-F1
Enzyme type: methyltransferase
Position of modification - modification: l:2922(2551) - Gm


PDB Structures:


6ELZ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.

Download RCSB-PDB Structures:

Pdb Files   6EM5.pdb  
Pdbx/mmCIF Files   6ELZ.cif   6EM5.cif   6YLX.cif   7OHR.cif   7OHV.cif  


Protein sequence:

MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVVIDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDCRSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENLVVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCKGFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGDNLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEFRSCIEDLKVLGKKDFKMILRWRKIAREILGIEVKDDAKTEIEVVPLTEEEQIEKDLQGLQEKQRLNVKRERRRKNEMKQKELQRMQMNMITPTDIGIEAASLGKESLFNLKTAEKTGILNDLAKGKKRMIFTDDELAKDNDIYIDENIMIKDKDSAADADDLESELNAMYSDYKTRRSERDAKFRAKQARGGDNEEEWTGFNEGSLEKKEEEGKDYIEDNDDEGVEGDSDDDEAITNLISKLKGQEGDHKLSSKARMIFNDPIFNNVEPDLPVNTVNDGIMSSESVGDISKLNKKRKHEEMHQKQDEADSSDESSSDDSDFEIVANDNASEEFDSDYDSEEEKNQTKKEKHSRDIDIATVEAMTLAHQLALGQKNKHDLVDEGFNRYTFRDTENLPDWFLEDEKEHSKINKPITKEAAMAIKEKIKAMNARPIKKVAEAKARKRMRAVARLEKIKKKAGLINDDSDKTEKDKAEEISRLMRKVTKKPKTKPKVTLVVASGRNKGLAGRPKGVKGKYKMVDGVMKNEQRALRRIAKKHHKKK

Comments:

Spb1 methylates the conserved G2922 (2551 in E.coli numbering) in the so-called A-loop (hairpin 92) of the peptidyltransferase center (domain V) in cytoplasmic pre-rRNA of large subunit rRNA into Gm. It also methylates U2921 (2552 in E. coli numbering) into Um, but only when snR52 guide RNA has been disrupted, otherwise U2921 is normally methylated within the nucleolus by Nop1 (snoRNP machinery). AdoMet is the methyl group donor. The human homolog has also been identified (FTSJ3).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:Gm RNA rRNA 2922 LSU-27S DOMAIN-V Prokaryotic Cytosol 15546625   
U:Um RNA rRNA 2921 LSU-27S DOMAIN-V Prokaryotic Cytosol 14636587   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P25582-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P25582-F1.cif  
DSSP Secondary Structures   P25582.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Lapeyre B, Purushothaman SK Mol Cell [details] 15546625 -
Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. Bonnerot C, Pintard L, Lutfalla G Mol Cell [details] 14636587 -
Spb1p is a putative methyltransferase required for 60S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Kressler D, Rojo M, Linder P, Cruz J Nucleic Acids Res [details] 10556316 -
Spb1p is a yeast nucleolar protein associated with Nop1p and Nop58p that is able to bind S-adenosyl-L-methionine in vitro. Pintard L, Kressler D, Lapeyre B Mol Cell Biol [details] 10648622 -