PDBsum entry 3v8v

Transferase

PDB id: 3v8v

Contents

Protein chains

664 a.a.

Ligands

GLC-TRV ×2

SAM ×4

Waters ×372

PDB id:

3v8v

Name:

Transferase

Title:

Crystal structure of bifunctional methyltransferase ycby (rlmlk) from escherichia coli, sam binding

Structure:

Ribosomal RNA large subunit methyltransferase l. Chain: a, b. Synonym: rlmlk, 23s rrna m2g2445 methyltransferase, rrna (guanine- n(2)-)-methyltransferase rlml. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: rlml. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.185 R-free: 0.247

Authors:

X.D.Su,K.T.Wang

Key ref:

K.T.Wang et al. (2012). Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res, 40, 5138-5148. PubMed id: 22362734

Date:

23-Dec-11 Release date: 29-Feb-12

Protein chains

P75864  (RLMKL_ECOLI) -  Ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (strain K12)

Seq: 702 a.a.

Struc: 664 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.173 - 23S rRNA (guanine(2445)-N(2))-methyltransferase.
• Reaction: guanosine₂₄₄₅ in 23S rRNA + S-adenosyl-L-methionine = N₂- methylguanosine₂₄₄₅ in 23S rRNA + S-adenosyl-L-homocysteine + H⁺

guanosine(2445) in 23S rRNA + S-adenosyl-L-methionine = N(2)- methylguanosine(2445) in 23S rRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAM) corresponds exactly)

• Enzyme class 3: E.C.2.1.1.264 - 23S rRNA (guanine(2069)-N(7))-methyltransferase.
• Reaction: guanosine₂₀₆₉ in 23S rRNA + S-adenosyl-L-methionine = N₂- methylguanosine₂₀₆₉ in 23S rRNA + S-adenosyl-L-homocysteine + H⁺

guanosine(2069) in 23S rRNA + S-adenosyl-L-methionine = N(2)- methylguanosine(2069) in 23S rRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAM) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Nucleic Acids Res 40:5138-5148 (2012)

PubMed id: 22362734

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA.

K.T.Wang, B.Desmolaize, J.Nan, X.W.Zhang, L.F.Li, S.Douthwaite, X.D.Su.

ABSTRACT

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.