Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanosine(37)-N1)-methyltransferase
Synonym: JW2588
GI: 67473571
Orf: b2607
COG: COG0336
UniProt: P0A873
Structures: | 1P9P |
Alpha Fold Predicted Structure: AF-P0A873-F1
Enzyme type: methyltransferase
Position of modification - modification: t:37 - m1G


PDB Structures:


1P9P

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The crystal structure of Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD) complexed with S-adenosyl homocysteine (AdoHcy) has been determined at 2.5A resolution. TrmD, which methylates G37 of tRNAs containing the sequence G36pG37, is a homo-dimer. Each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain. The two bound AdoHcy moieties are buried at the bottom of deep clefts. The dimer structure appears integral to the formation of the catalytic center of the enzyme and this arrangement strongly suggests that the anticodon loop of tRNA fits into one of these clefts for methyl transfer to occur. In addition, adjacent hydrophobic sites in the cleft delineate a defined pocket, which may accommodate the GpG sequence during catalysis. The dimer contains two deep trefoil peptide knots and a peptide loop extending from each knot embraces the AdoHcy adenine ring. Mutational analyses demonstrate that the knot is important for AdoMet binding and catalytic activity, and that the C-terminal domain is not only required for tRNA binding but plays a functional role in catalytic activity.

Download RCSB-PDB Structures:

Pdb Files   1P9P.pdb  
Pdbx/mmCIF Files   1P9P.cif  


Protein sequence:

MWIGIISLFPEMFRAITDYGVTGRAVKNGLLSIQSWSPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGIDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVSRFIPGVLGHEASATEDSFAEGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA

Comments:

AdoMet is the methyl group donor. SPOUT superfamily.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m1G RNA tRNA 37 CAG CAG tRNALeuCAG anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 GAG GAG tRNALeuGAG anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 UAGd UAGd tRNALeuUAGd anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 CGGd CGGd tRNAProCGGd anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 GGGd GGGd tRNAProGGGd anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 UGGd UGGd tRNAProUGGd anticodon-stem loop Prokaryotic Cytosol
G:m1G RNA tRNA 37 CCG CCG tRNAArgCCG anticodon-stem loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P0A873-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0A873-F1.cif  
DSSP Secondary Structures   P0A873.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The structural gene (trmD) for the tRNA(m1G)methyltransferase is part of a four polypeptide operon in Escherichia coli K-12. Bystrom AS, Bjork GR Mol Gen Genet [details] 6298574 -
Insights into catalysis by a knotted TrmD tRNA methyltransferase. Elkins PA, Watts JM, Zalacain M, van Thiel A, Vitazka PR, Redlak M, Andraos-Selim C, Rastinejad F, Holmes WM J Mol Biol [details] 14583191 -
Control of catalytic cycle by a pair of analogous tRNA modification enzymes. Christian T, Lahoud G, Liu C, Hou YM J Mol Biol [details] 20452364 -