Modomics - A Database of RNA Modifications

ID Card:

Full name: rRNA N6-adenosine-methyltransferase
Synonym: DC3, HSPC133
GI: 74761664
UniProt: Q9NRN9
Structures: | 6H2U | 6H2V |
Alpha Fold Predicted Structure: AF-Q9NRN9-F1
Complex: TRMT112
Enzyme type: methyltransferase


PDB Structures:


6H2U

Structure Description:

Title: Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 1.6A resolution
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 1.6
R value free: 0.215
R value observed: 0.187
R value work: 0.186

Abstract of the PDB Structure's related Publication:

N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5-TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5-TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.

Download RCSB-PDB Structures:

Pdb Files   6H2U.pdb   6H2V.pdb  
Pdbx/mmCIF Files   6H2U.cif   6H2V.cif  


Protein sequence:

MKKVRLKELESRLQQVDGFEKPKLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNRNAEEFELTNIDMVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGTDMAFLKTALEMARTAVYSLHKSSTREHVQKKAAEWKIKIDIIAELRYDLPASYKFHKKKSVDIEVDLIRFSF

Comments:

Catalytic subunit of a heterodimer with TRMT112, which specifically methylates the 6th position of adenine in position 1832 of 18S rRNA





Alpha Fold Predicted Structure:




Parsing response... [198292/198292]


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Protein sequence:

M K K V R L K E L E S R L Q Q V D G F E K P K L L L E Q Y P T R P H I A A C M L Y T I H N T Y D D I E N K V V A D L G C G C G V L S I G T A M L G A G L C V G F D I D E D A L E I F N R N A E E F E L T N I D M V Q C D V C L L S N R M S K S F D T V I M N P P F G T K N N K G T D M A F L K T A L E M A R T A V Y S L H K S S T R E H V Q K K A A E W K I K I D I I A E L R Y D L P A S Y K F H K K K S V D I E V D L I R F S F
20406080100120140160180200MKKVRLKELESRLQQVDGFEKPKLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNRNAEEFELTNIDMVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGTDMAFLKTALEMARTAVYSLHKSSTREHVQKKAAEWKIKIDIIAELRYDLPASYKFHKKKSVDIEVDLIRFSFSequenceGHTSN

Enter the variants

Position

Original

Variant

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-Q9NRN9-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9NRN9-F1.cif  
DSSP Secondary Structures   Q9NRN9.dssp  





Publications: