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The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.

Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O - Nucleic Acids Res. (2014)

Bottom Line: The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology.Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P.Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan.

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Overall structure of YfcM, seen from two perpendicular directions. The structure is depicted by a rainbow-colored ribbon model. Disordered loops are represented as dashed lines.
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Figure 1: Overall structure of YfcM, seen from two perpendicular directions. The structure is depicted by a rainbow-colored ribbon model. Disordered loops are represented as dashed lines.

Mentions: To reveal the mechanism of EF-P hydroxylation catalyzed by YfcM, the crystal structure of YfcM was determined at 1.45 Å resolution by the MAD method. In the crystal, YfcM exists as a monomer. The structure consists of five α-helices (α1–α5) and a β sheet composed of three β strands (β1–β3) (Figure 1). The residues forming the loop between α2 and α3 were removed by the trypsin digestion during the crystallization, as confirmed by N-terminal sequencing and MALDI-TOF mass spectrometry analyses (28). As a result, residues Gly68–Ser92 are not modeled because of the lack of electron density. In addition, the residues Met1-Asn2, Val118-Asp130 and Ala180 to the C-terminus are also structurally disordered.


The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.

Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O - Nucleic Acids Res. (2014)

Overall structure of YfcM, seen from two perpendicular directions. The structure is depicted by a rainbow-colored ribbon model. Disordered loops are represented as dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231759&req=5

Figure 1: Overall structure of YfcM, seen from two perpendicular directions. The structure is depicted by a rainbow-colored ribbon model. Disordered loops are represented as dashed lines.
Mentions: To reveal the mechanism of EF-P hydroxylation catalyzed by YfcM, the crystal structure of YfcM was determined at 1.45 Å resolution by the MAD method. In the crystal, YfcM exists as a monomer. The structure consists of five α-helices (α1–α5) and a β sheet composed of three β strands (β1–β3) (Figure 1). The residues forming the loop between α2 and α3 were removed by the trypsin digestion during the crystallization, as confirmed by N-terminal sequencing and MALDI-TOF mass spectrometry analyses (28). As a result, residues Gly68–Ser92 are not modeled because of the lack of electron density. In addition, the residues Met1-Asn2, Val118-Asp130 and Ala180 to the C-terminus are also structurally disordered.

Bottom Line: The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology.Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P.Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan.

Show MeSH
Related in: MedlinePlus