Modomics - A Database of RNA Modifications

ID Card:

Full name:	Multisite-specific tRNA:(cytosine-C(5))-methyltransferase
Synonym:	Ncl1p
GI:	586408
Orf:	YBL024W
COG:	COG0144
UniProt:	P38205
Alpha Fold Predicted Structure:	AF-P38205-F1
Enzyme type:	methyltransferase
Position of modification - modification:	t:34 - m5C t:40 - m5C t:48 - m5C

Protein sequence:

MARRKNFKKGNKKTFGARDDSRAQKNWSELVKENEKWEKYYKTLALFPEDQWEEFKKTCQAPLPLTFRITGSRKHAGEVLNLFKERHLPNLTNVEFEGEKIKAPVELPWYPDHLAWQLDVPKTVIRKNEQFAKTQRFLVVENAVGNISRQEAVSMIPPIVLEVKPHHTVLDMCAAPGSKTAQLIEALHKDTDEPSGFVVANDADARRSHMLVHQLKRLNSANLMVVNHDAQFFPRIRLHGNSNNKNDVLKFDRILCDVPCSGDGTMRKNVNVWKDWNTQAGLGLHAVQLNILNRGLHLLKNNGRLVYSTCSLNPIENEAVVAEALRKWGDKIRLVNCDDKLPGLIRSKGVSKWPVYDRNLTEKTKGDEGTLDSFFSPSEEEASKFNLQNCMRVYPHQQNTGGFFITVFEKVEDSTEAATEKLSSETPALESEGPQTKKIKVEEVQKKERLPRDANEEPFVFVDPQHEALKVCWDFYGIDNIFDRNTCLVRNATGEPTRVVYTVCPALKDVIQANDDRLKIIYSGVKLFVSQRSDIECSWRIQSESLPIMKHHMKSNRIVEANLEMLKHLLIESFPNFDDIRSKNIDNDFVEKMTKLSSGCAFIDVSRNDPAKENLFLPVWKGNKCINLMVCKEDTHELLYRIFGIDANAKATPSAEEKEKEKETTESPAETTTGTSTEAPSAAN

Comments:

S-Adenosyl methionine (SAM or AdoMet) consists of an adenosyl cation attached to the sulfur methionine. It is synthesized from ATP and methionine by S-Adenosylmethionine synthetase enzyme through the the reaction of ATP with L-methionine and water forming as catalytical product S-adenosyl-L-methionine. SAM is a common cosubstrate involved in several reactions, among which methyl group transfers. Trm4 is a multisite-specific—monomeric enzyme using SAM as a cosubstrate. In most mature tRNAs modifies either 48 or 49, and only two tRNAs Trm4 modifies either 34 or 40, but only before the intron is removed. In yeast, the activity of Trm4 and consequently the degree of m5C modification in tRNALeu depends on certain stress conditions (presence of H2O2), which causes selective translation of mRNA from genes enriched in the TTG codon.

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	Transcript Name	Transcript Region	Cellular Localization
C:m5C	tRNA (t)	tRNA	34	CUA	?UA	tRNA^Leu_CUA	wobble - position	Nucleus
C:m5C	RNA	tRNA	40	GAA	GAA	tRNA^Phe_GAA	anticodon-stem loop	Nucleus
C:m5C	RNA	tRNA	48	GUU	GUU	tRNA^Asn_GUU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	GCA	GCA	tRNA^Cys_GCA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	IAU	IAU	tRNA^Ile_IAU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	UAU	UAU	tRNA^Ile_UAU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	UAG	UAG	tRNA^Leu_UAG	V-loop	Nucleus
C:m5C	RNA	tRNA	48	CAA	CAA	tRNA^Leu_CAA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	UAA	UAA	tRNA^Leu_UAA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	SUU	SUU	tRNA^Lys_SUU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	CAU	CAU	tRNA^Met_CAU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	CGA	CGA	tRNA^Ser_CGA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	UGA	UGA	tRNA^Ser_UGA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	IGA	IGA	tRNA^Ser_IGA	V-loop	Nucleus
C:m5C	RNA	tRNA	48	IGU	IGU	tRNA^Thr_IGU	V-loop	Nucleus
C:m5C	RNA	tRNA	48	GUA	GUA	tRNA^Tyr_GUA	V-loop	Nucleus
C:m5C	RNA	tRNA	49	ICG	ICG	tRNA^Arg_ICG	V-loop	Nucleus
C:m5C	RNA	tRNA	49	GUC	GUC	tRNA^Asp_GUC	V-loop	Nucleus
C:m5C	RNA	tRNA	49	CUC	CUC	tRNA^Glu_CUC	V-loop	Nucleus
C:m5C	RNA	tRNA	49	GCC	GCC	tRNA^Gly_GCC	V-loop	Nucleus
C:m5C	RNA	tRNA	49	GUG	GUG	tRNA^His_GUG	V-loop	Nucleus
C:m5C	RNA	tRNA	49	GAA	GAA	tRNA^Phe_GAA	V-loop	Nucleus
C:m5C	RNA	tRNA	49	UAC	UAC	tRNA^Val_UAC	V-loop	Nucleus
C:m5C	RNA	tRNA	49	CAC	CAC	tRNA^Val_CAC	V-loop	Nucleus
C:m5C	RNA	tRNA	49	IAC	IAC	tRNA^Val_IAC	V-loop	Nucleus

Alpha Fold Predicted Structure:

Clear Selection and Reset Camera

Protein sequence:

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

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-P38205-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-P38205-F1.cif
DSSP Secondary Structures	P38205.dssp

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme.	Motorin Y, Grosjean H	RNA	[details]	10445884	-
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins.	Chan CT, Pang YL, Deng W, Babu IR, Dyavaiah M, Begley TJ, Dedon PC...	Nat Commun	[details]	22760636	-
Trm4 and Nsun2 RNA:mC Methyltransferases Form Metabolite-Dependent, Covalent Adducts with Previously Methylated RNA.	Moon HJ, Redman KL...	Biochemistry	[details]	25375641	-