Modomics - A Database of RNA Modifications

ID Card:

Full name:	tRNA (guanosine(18)-2′-O)-methyltransferase
GI:	74627230
Orf:	YDL112W
COG:	COG0566
UniProt:	Q07527
Alpha Fold Predicted Structure:	AF-Q07527-F1
Enzyme type:	methyltransferase
Position of modification - modification:	t:18 - Gm

Protein sequence:

MVGGALICKYLPREEQLKLISDLIQNDSLEEVLELIETSPLDITTDSNIETPIFEKITEQVIAYASIDGEAREMFRSSRAEMNKALRTSAQLLCCLPSVWHKFQVWMSYRLNDIISENYKHLFNDNFGKKIVQPFFDSFAEEQNANIKHENLHLDILSLLHYLEVVYLFDECKNGISSKCLDFIIVPLLGCNSEEIADSCSKLMRWHIKYLSKCCNTDSNFDKLIWTFIKQLYAEGSQQAWKQKNSLSFLLRFLLAAELSPELITYIKTDAYWRHIQTELDNDVHEHRKLALSILKLTIQKLSSHGITLQTTFYKCNDLANIEMLGSWKKFTTLYEMIALDTSLNQIQAAKQDIIKIFDNEHLHHSWGLILLSTGLKSSMESVRKYMMTLMFSITNMSAFSSNLPLLTKTLLPAAMSAHYFDVKGVSCPHGEKLSLFVNNLLSQTTEGISDILFEILKLLVEKGTSFDPSRIYLSYGILVFFQNNKQKTINSDHLSLIRKLYDFAAEEEVLETTIQTIYLKFLLYIDPSVSASELLFTLVSHIKLKGGTYKYVEPLFEDYRDLAVSHFDDLQAKENLTTNIGKDTIFDLLASIIFDFKDIDITPDFLIEVAKSKQDIPVYTSKAVTFLTQLLSGEPSNGYTYENATALLSYPNFTISTWKSINVNNLFKSVMEKFSLDKFKFFAEIYQKTYECRFDTIELNFNDLLSLYEMVKKSANQCSRESFKVKDSAYSSYFELLNTFLKTYALNRDSSEGNDDELHILLRLVDENINKDNGNYLGNLAVCKLLYFIIDSYIHCSTSVSDDDIFIVKFIFEKFSFIWECINSERLVLKERDLHLMLIKGLFHPVILYFGSNQYIDTLTSKLEEHAQTIISLSYSRRSLLPLLGSQLRVFMKFYGKLLREDVNYWWLINIIVGVFKQPQMDVNLYKLKPVISSLFDHKLNNYYIKGDELYEKVYGPDEILARVSIIDSILYANDQLKIRLIEKVTEKTNALYAIKRTDGAEALQRLLQWQLLLLSLLTTNEKKLSETSMIRILKSIEDESSPLVRVYKEWFISSKVVDYYKTGNPKFAEDYLFSLLEDHSKPVFVVSAEKICFMVLKDLRNDEKKYGFTQLLDRFICTLVPNAASNKPLVRHFSNSLIISLWPTFKAYLSDHTLRNIIENLYSNAKKTQIFGQYRAGDANIWDLKGDRKLTNMFGGVLKKVTDHDCPYISESVFEKYLQEKDIVPIGTDERSLWLDKRDTNTESVNNANISCDTSPLQTKSGAWETVLDLDNKKSNDVVTRSELIVVSSLVDKPPNLGGICRLCDVLGVGLLTVQDIKVKNHPQFKNVAVTADRWMPMEEVALDEIASFMKEKKKEGYTLIGLEQTDKSVKLDNNFQFPKKSLILLGTEAFGIPGTLLSELDLCLEIQQFGVIRSMNIQTATAVIVHSYTVQHM

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 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. SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual fold with a deep topological knot ( Tkaczuk et al. 2007). Trm3 is a site specific enzyme belonging to this family using SAM as a cosubstrate to catalyze the formation of 2'-O-methylguanosine at position 18 (Gm18) in all the intron the intron-less yeast tRNAs ( Cavaille et al. 1999).

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	Transcript Name	Transcript Region	Cellular Localization	References
G:Gm	RNA	tRNA	18	UAG	UAG	tRNA^Leu_UAG	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	CAA	CAA	tRNA^Leu_CAA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	UAA	UAA	tRNA^Leu_UAA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	GUG	GUG	tRNA^His_GUG	D-loop	Mitochondrion and Cytoplasm	9917067
G:Gm	RNA	tRNA	18	GUA	GUA	tRNA^Tyr_GUA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	CGA	CGA	tRNA^Ser_CGA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	UGA	UGA	tRNA^Ser_UGA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	IGA	IGA	tRNA^Ser_IGA	D-loop	Cytoplasm	9917067
G:Gm	RNA	tRNA	18	CCA	CCA	tRNA^Trp_CCA	D-loop	Cytoplasm	9917067

Alpha Fold Predicted Structure:

Clear Selection and Reset Camera

Protein sequence:

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

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-Q07527-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-Q07527-F1.cif
DSSP Secondary Structures	Q07527.dssp

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs.	Cavaille J, Chetouani F, Bachellerie JP	RNA	[details]	9917067	-