Modomics - A Database of RNA Modifications

ID Card:

Full name:	Ribosomal RNA small subunit methyltransferase I
Synonym:	yraL
GI:	1789535
COG:	COG0313
UniProt:	P67087
Structures:	\| 5HW4 \|
Alpha Fold Predicted Structure:	AF-P67087-F1
Enzyme type:	methyltransferase
Position of modification - modification:	s:1403(1403) - m4Cm

PDB Structures:

5HW4

Structure Description:

Title:	Crystal structure of Escherichia coli 16S rRNA methyltransferase RsmI in complex with AdoMet
Classification:	TRANSFERASE
Technique:	X-Ray Diffraction
Resolution:	2.21
R value free:	0.230
R value observed:	0.204
R value work:	0.203

Abstract of the PDB Structure's related Publication:

RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD) and a C-terminal catalytic domain (CTD) with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC) assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.

Download RCSB-PDB Structures:

Pdb Files	5HW4.pdb 5IW5.pdb
Pdbx/mmCIF Files	5HW4.cif 5IW5.cif

Protein sequence:

MKQHQSADNSQGQLYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFGINARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPLPGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAEPRTLIFYESTHRLLDSLEDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDENRRKGEMVLIVEGHKAQEEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALYKYALEQQG

Comments:

RsmI catalyzes 2’-O-ribose methylation of cytidine C1402 (Cm) in helix 44 within the decoding center of 16S rRNA. AdoMet is the methyl group donor and the 30S subunit (not the naked 16 rRNA) is the substrate. This enzyme is conserved in almost all species of bacteria. Together with methyltransferase TrmH, it allows the formation of very conserved m4Cm. Notice, in yeast, human and Arabidopsis the ribose methylation of equivalent C in 18S rRNA is catalyzed by a snoRNA-guided methylation machinery.

Search:

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	Amino Acid Change	Transcript Name	Transcript Region	Cellular Localization	References
C:Cm	RNA	rRNA	1402				SSU-16S		Prokaryotic Cytosol	19965768
m4C:m4Cm	RNA	rRNA	1402				SSU-16S		Prokaryotic Cytosol	19965768


C:Cm
m4C:m4Cm

Showing 1 to 2 of 2 entries

Alpha Fold Predicted Structure:

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Protein sequence:

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

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-P67087-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-P67087-F1.cif
DSSP Secondary Structures	P67087.dssp

Publications:

Search:

Title	Authors	Journal	Details	PubMed Id	DOI
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.	Kimura S, Suzuki T	Nucleic Acids Res	[details]	19965768	-
Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus.	Guymon R, Pomerantz SC, Crain PF, McCloskey JA	Biochemistry	[details]	16605256	-
Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli.	Zhao M, Wang L, Zhang H, Dong Y, Gong Y, Zhang L, Wang J...	Acta Crystallogr F Struct Biol Commun	[details]	25195904	-


Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus.
Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli.

Showing 1 to 3 of 3 entries