Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmCD
GI: 218929828
COG: COG4121
UniProt: Q8ZD36
Structures: | 3PVC | 3SGL |
Alpha Fold Predicted Structure: AF-Q8ZD36-F1
Enzyme type: methyltransferase/oxidoreductase
Position of modification - modification: t:34 - mnm5s2U
t:34 - mnm5U


PDB Structures:


3PVC

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34).

Download RCSB-PDB Structures:

Pdb Files   3PVC.pdb   3SGL.pdb  
Pdbx/mmCIF Files   3PVC.cif   3SGL.cif  


Protein sequence:

MNQRPIQTATLSWNEQGTPVSEQFGDIYFSNEDGLEETHHVFLKGNGFPARFASHPQQSCIFAETGFGTGLNFLTLWRDFALFRQQSPNATLRRLHYISFEKYPLHVADLASAHARWPELASFAEQLRAQWPLPLAGCHRILLADGAITLDLWFGDVNTLLPTLDDSLNNQVDAWFLDGFAPAKNPDMWNEQLFNAMARMTRPGGTFSTFTAAGFVRRGLQQAGFNVTKVKGFGQKREMLTGTLPQQIHAPTAPWYHRPAATRCDDIAIIGGGIVSALTALALQRRGAVVTLYCADAQPAQGASGNRQGALYPLLNGKNDALETFFTSAFTFARRQYDQLLEQGIAFDHQWCGVSQLAFDDKSRGKIEKMLHTQWPVEFAEAMSREQLSELAGLDCAHDGIHYPAGGWLCPSDLTHALMMLAQQNGMTCHYQHELQRLKRIDSQWQLTFGQSQAAKHHATVILATGHRLPEWEQTHHLPLSAVRGQVSHIPTTPVLSQLQQVLCYDGYLTPVNPANQHHCIGASYQRGDIATDFRLTEQQENRERLLRCLPQVSWPQQVDVSDNQARCGVRCAIRDHLPMVGAVPDYAATLAQYQDLSRRIQHGGESEVNDIAVAPVWPELFMVGGLGSRGLCSAPLVAEILAAQMFGEPLPLDAKTLAALNPNRFWIRKLLKGRPVQTRSPATQESSR

Comments:

Homologue of E. coli MnmCD. In E.coli (and many other bacteria) it is a bifunctional enzyme, composed of two domains that catalyze two successive reactions at the uridine wobble position 34 in tRNA: first a deacetylation reaction of cmnm5U into nm5U, then methylation of the amine group of nm5U to form mnm5U. In other organisms they may be unlinked (separate proteins), then identified as MnmC for the deacetylase and MnmD for the methylase. In certain bacteria, the catalytic domain for the deacetylation reaction is absent in their genome and only the gene coding for MnmD is present. In other bacteria, MnmC and MnmD are both present.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M N Q R P I Q T A T L S W N E Q G T P V S E Q F G D I Y F S N E D G L E E T H H V F L K G N G F P A R F A S H P Q Q S C I F A E T G F G T G L N F L T L W R D F A L F R Q Q S P N A T L R R L H Y I S F E K Y P L H V A D L A S A H A R W P E L A S F A E Q L R A Q W P L P L A G C H R I L L A D G A I T L D L W F G D V N T L L P T L D D S L N N Q V D A W F L D G F A P A K N P D M W N E Q L F N A M A R M T R P G G T F S T F T A A G F V R R G L Q Q A G F N V T K V K G F G Q K R E M L T G T L P Q Q I H A P T A P W Y H R P A A T R C D D I A I I G G G I V S A L T A L A L Q R R G A V V T L Y C A D A Q P A Q G A S G N R Q G A L Y P L L N G K N D A L E T F F T S A F T F A R R Q Y D Q L L E Q G I A F D H Q W C G V S Q L A F D D K S R G K I E K M L H T Q W P V E F A E A M S R E Q L S E L A G L D C A H D G I H Y P A G G W L C P S D L T H A L M M L A Q Q N G M T C H Y Q H E L Q R L K R I D S Q W Q L T F G Q S Q A A K H H A T V I L A T G H R L P E W E Q T H H L P L S A V R G Q V S H I P T T P V L S Q L Q Q V L C Y D G Y L T P V N P A N Q H H C I G A S Y Q R G D I A T D F R L T E Q Q E N R E R L L R C L P Q V S W P Q Q V D V S D N Q A R C G V R C A I R D H L P M V G A V P D Y A A T L A Q Y Q D L S R R I Q H G G E S E V N D I A V A P V W P E L F M V G G L G S R G L C S A P L V A E I L A A Q M F G E P L P L D A K T L A A L N P N R F W I R K L L K G R P V Q T R S P A T Q E S S 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-Q8ZD36-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8ZD36-F1.cif  
DSSP Secondary Structures   Q8ZD36.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. Kim J, Almo SC BMC Struct Biol [details] 23617613 -

Links:

_PubMed_