Modomics - A Database of RNA Modifications

ID Card:

Full name: 5-methylcytosine rRNA methyltransferase NSUN4, mitochondrial
Synonym: NOL1/NOP2/Sun domain family member 4
GI: 370879165
UniProt: Q96CB9
Structures: | 4FP9 | 4FZV | 7O9K | 7O9M | 7ODR | 7ODS | 7ODT | 7OF0 | 7OF5 | 7OF7 | 7OIC | 7PD3 |
Alpha Fold Predicted Structure: AF-Q96CB9-F1
Enzyme type: methyltransferase
Position of modification - modification: s:841(None) - m5C


PDB Structures:


4FP9

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. Mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. This complex process is evolutionary conserved and involves several RNA processing and modification steps required for correct ribosomal RNA maturation. We recently showed that a member of the mitochondrial transcription termination factor (MTERF) family of proteins, MTERF4, recruits NSUN4, a 5-methylcytosine RNA methyltransferase, to the large ribosomal subunit in a process crucial for mitochondrial ribosome biogenesis. Here, we describe the 3D crystal structure of the human MTERF4-NSUN4 complex determined to 2.9 Å resolution. MTERF4 is composed of structurally repeated MTERF-motifs that form a nucleic acid binding domain. NSUN4 lacks an N- or C-terminal extension that is commonly used for RNA recognition by related RNA methyltransferases. Instead, NSUN4 binds to the C-terminus of MTERF4. A positively charged surface forms an RNA binding path from the concave to the convex side of MTERF4 and further along NSUN4 all of the way into the active site. This finding suggests that both subunits of the protein complex likely contribute to RNA recognition. The interface between MTERF4 and NSUN4 contains evolutionarily conserved polar and hydrophobic amino acids, and mutations that change these residues completely disrupt complex formation. This study provides a molecular explanation for MTERF4-dependent recruitment of NSUN4 to ribosomal RNA and suggests a unique mechanism by which other members of the large MTERF-family of proteins can regulate ribosomal biogenesis.

Download RCSB-PDB Structures:

Pdb Files   4FP9.pdb   4FZV.pdb   7ODT.pdb   7OF0.pdb  
Pdbx/mmCIF Files   4FP9.cif   4FZV.cif   7O9K.cif   7O9M.cif   7ODR.cif   7ODS.cif   7OF0.cif   7OF5.cif   7OF7.cif   7OIC.cif   7PD3.cif  


Protein sequence:

MAALTLRGVRELLKRVDLATVPRRHRYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLWPSIRVSLLSEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAPSPASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLALGLQPGDIVLDLCAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILHSYVPEEIRDGNQVRVTSWDGRKWGELEGDTYDRVLVDVPCTTDRHSLHEEENNIFKRSRKKERQILPVLQVQLLAAGLLATKPGGHVVYSTCSLSHLQNEYVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQVGELVIPNLMANFGPMYFCKMRRLT

Comments:





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q96CB9-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q96CB9-F1.cif  
DSSP Secondary Structures   Q96CB9.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. Metodiev MD, Spåhr H, Loguercio Polosa P, Meharg C, Becker C, Altmueller J, Habermann B, Larsson NG, Ruzzenente B. PLoS Genet. [details] 24516400 10.1371/journal.pgen.1004110
Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis. Spåhr H, Habermann B, Gustafsson CM, Larsson NG, Hallberg BM. Proc Natl Acad Sci U S A [details] 22949673 10.1073/pnas.1210688109
MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cámara Y, Asin-Cayuela J, Park CB, Metodiev MD, Shi Y, Ruzzenente B, Kukat C, Habermann B, Wibom R, Hultenby K, Franz T, Erdjument-Bromage H, Tempst P, Hallberg BM, Gustafsson CM, Larsson NG. Cell Metab. [details] 21531335 10.1016/j.cmet.2011.04.002