Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA methyltransferase 112 homolog
Synonym: TRMT112
GI: 7705477
Orf: AD-001, HSPC152, HSPC170
COG: COG2835
UniProt: Q9UI30
Structures: | 6G4W | 6H1D | 6H1E | 6H2U | 6H2V | 6K0X | 6KHS | 6KHR | 6KMS | 6PED |
Alpha Fold Predicted Structure: AF-Q9UI30-F1
Enzyme type: methyltransferase


PDB Structures:


6G4W

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.

Download RCSB-PDB Structures:

Pdb Files   6G4W.pdb   6H1D.pdb   6H1E.pdb   6H2U.pdb   6H2V.pdb   6K0X.pdb   6KHR.pdb   6KHS.pdb   6KMS.pdb   6PED.pdb  
Pdbx/mmCIF Files   6G4W.cif   6H1D.cif   6H1E.cif   6H2U.cif   6H2V.cif   6K0X.cif   6KHR.cif   6KHS.cif   6KMS.cif   6PED.cif  


Protein sequence:

MKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVARMIPKVEWSAFLEAADNLRLIQVPKGPVEGYEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETES

Comments:

The tRNA methyltransferase subunit 11-2 activates rRNA, tRNA, and protein methyltransferase. Forming a heterodimer with WBSCR22, it methylates guanosine, in position 1639 of human rRNA subunit 18S, on its N7 position (cap 0) (Zorbas et al. 2015 ). Acting in concert with THUMPD3, it catalyzes the formation of N2-methylguanosine on the 6th and 10th positions of a broad range of tRNA substrates, and specifically modifying the 7th position of tRNA (Trp) (Yang et al. 2021). It, moreover, forms a heterodimer with ALKBH8 catalyzing the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA species (Fu et al. 2010). Considering other RNA types, together with METTL5, it specifically methylates rRNA 18S A1832 in its 6th position (Yu et al. 2021, Sepich-Poore. et al 2022, van Tran et al. 2019). It is Trm112 yeast's homologue.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
GpppN:m7GpppN RNA rRNA 1639 small rRNA subunit 18S Nucleus - Nucleoplasm 25851604   
G:m2G RNA tRNA 6 CCC CCC tRNAGlyCCC - 1 5'-stem loop Cytosol 34669960   
G:m2G RNA tRNA 6 CCC CCC tRNAGlyCCC-2 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 6 GCC GCC tRNAGlyGCC 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 6 CAA CAA tRNALeuCAA 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 6 CUU CUU tRNALysCUU 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 6 GUA GUA tRNATyrGUA 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 6 CAU CAU tRNAMetCAU 5'-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 10 CAA CAA tRNALeuCAA D-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 10 CUU CUU tRNALysCUU D-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 10 GUA GUA tRNATyrGUA D-stem loop Cytoplasm 34669960   
G:m2G RNA tRNA 10 CAU CAU tRNAMetCAU D-stem loop Cytoplasm 34669960   
cm5U:mcm5U RNA tRNA 34 ◊CG 1CG tRNAArgUCG wobble - position Cytoplasm 20308323   
cm5U:mcm5U RNA tRNA 34 ◊CC 1CC tRNAGlyUCC wobble - position Cytoplasm 20308323   
A:m6A RNA rRNA 1832 small rRNA subunit 18S Subnuclear 31328227    33428944    35033535   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q9UI30-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9UI30-F1.cif  
DSSP Secondary Structures   Q9UI30.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Songe-Moller L, van den Born E, Leihne V, Vagbo CB, Kristoffersen T, Krokan HE, Kirpekar F, Falnes PO, Klungland A Mol Cell Biol [details] 20123966 -