PDBsum entry 2zwa

Transferase

PDB id: 2zwa

Contents

Protein chains

672 a.a. *

Ligands

SAH ×2

CIT ×2

EDO ×6

Waters ×1543

* Residue conservation analysis

PDB id:

2zwa

Name:

Transferase

Title:

Crystal structure of tRNA wybutosine synthesizing enzyme tyw4

Structure:

Leucine carboxyl methyltransferase 2. Chain: a, b. Synonym: tRNA wybutosine-synthesizing protein 4. Engineered: yes

Source:

Saccharomyces cerevisiae. Organism_taxid: 4932. Gene: ppm2, tyw4, yol141w. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.174 R-free: 0.211

Authors:

Y.Suzuki,A.Noma,T.Suzuki,R.Ishitani,O.Nureki

Key ref:

Y.Suzuki et al. (2009). Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res, 37, 2910-2925. PubMed id: 19287006

Date:

01-Dec-08 Release date: 02-Jun-09

Protein chains

Q08282  (TYW4_YEAST) -  tRNA wybutosine-synthesizing protein 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 695 a.a.

Struc: 672 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.290 - tRNA(Phe) [7-(3-amino-3-carboxypropyl)wyosine(37)-O]-methyltransferase.
• Reaction: 7-[(3S)-3-amino-3-carboxypropyl]wyosine₃₇ in tRNA(Phe) + S-adenosyl-L- methionine = 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine₃₇ in tRNA(Phe) + S-adenosyl-L-homocysteine

7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L- methionine = 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly)

• Enzyme class 3: E.C.2.3.1.231 - tRNA(Phe) {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine(37)-N}-
• Reaction: 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine₃₇ in tRNA(Phe) + S-adenosyl-L-methionine + CO2 = wybutosine₃₇ in tRNA(Phe) + S-adenosyl- L-homocysteine + 2 H⁺

7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + CO2 = wybutosine(37) in tRNA(Phe) + S-adenosyl- L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + 2 × H(+)

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 37:2910-2925 (2009)

PubMed id: 19287006

Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.

Y.Suzuki, A.Noma, T.Suzuki, R.Ishitani, O.Nureki.

ABSTRACT

Wybutosine (yW), one of the most complicated modified nucleosides, is found in the anticodon loop of eukaryotic phenylalanine tRNA. This hypermodified nucleoside ensures correct codon recognition by stabilizing codon-anticodon pairings during the decoding process in the ribosome. TYW4 is an S-adenosylmethionine (SAM)-dependent enzyme that catalyzes the final step of yW biosynthesis, methylation and methoxycarbonylation. However, the structural basis for the catalytic mechanism by TYW4, and especially that for the methoxycarbonylation, have remained elusive. Here we report the apo and cofactor-bound crystal structures of yeast TYW4. The structures revealed that the C-terminal domain folds into a beta-propeller structure, forming part of the binding pocket for the target nucleoside. A comparison of the apo, SAM-bound, and S-adenosylhomocysteine-bound structures of TYW4 revealed a drastic structural change upon cofactor binding, which may sequester solvent from the catalytic site during the reaction and facilitate product release after the reaction. In conjunction with the functional analysis, our results suggest that TYW4 catalyzes both methylation and methoxycarbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide.