Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 May 11:5:10100.
doi: 10.1038/srep10100.

Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase

Sheng-Chia Chen  1 , Chi-Hung Huang  1 , Shu-Jung Lai  2 , Jai-Shin Liu  3 , Pin-Kuei Fu  4 , Shih-Ting Tseng  5 , Chia Shin Yang  1 , Mei-Chin Lai  2 , Tzu-Ping Ko  6 , Yeh Chen  7
Affiliations

Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase

Sheng-Chia Chen et al. Sci Rep. .

Abstract

Streptosporangium sibiricum SibL catalyzes the methyl transfer from S-adenosylmethionine (SAM) to 3-hydroxykynurenine (3-HK) to produce S-adenosylhomocysteine (SAH) and 3-hydroxy-4-methyl-kynurenine for sibiromycin biosynthesis. Here, we present the crystal structures of apo-form Ss-SibL, Ss-SibL/SAH binary complex and Ss-SibL/SAH/3-HK ternary complex. Ss-SibL is a homodimer. Each subunit comprises a helical N-terminal domain and a Rossmann-fold C-terminal domain. SAM (or SAH) binding alone results in domain movements, suggesting a two-step catalytic cycle. Analyses of the enzyme-ligand interactions and further mutant studies support a mechanism in which Tyr134 serves as the principal base in the transferase reaction of methyl group from SAM to 3-HK.

PubMed Disclaimer

Figures

Figure 1
Figure 1
A schematic representation of the Ss-SibL enzymatic reaction.
Figure 2
Figure 2
Structure of the Ss-SibL protein. (a) Ribbon representation of the dimeric Ss-SibL structure is viewed down its 2-fold axis. Subunits A and B are shown in green and blue, respectively. The SAH and 3-HK are shown as magenta and orange stick models. (b) and (c) The composite omit maps for the ligands in the binary and ternary complex crystals are contoured at the 1.5 σ level and drawn as grey mesh presentations. Each subunit of the bound Ss-SibL includes both SAH and 3-HK in the cleft. SAH is depicted as sticks with the carbon, oxygen, nitrogen, and sulfur atoms in magenta, red, blue, and yellow, whereas 3-HK is illustrated with the carbon, oxygen, and nitrogen in orange, red, and blue, respectively.
Figure 3
Figure 3
The conformational change of Ss-SibL. Structures of Ss-SibL reveal that conformational change of the C-terminal domain triggered by SAH binding, followed by 3-HK binding that does not cause any major structural change.
Figure 4
Figure 4
Ligand interactions in the active site. In (a) the SAH-interacting residues via hydrogen bonds are shown as stick models. The nitrogen, oxygen, and carbon atoms are colored blue, red, and green. The bound SAH is shown with magenta carbons. Black dashes represents the potential hydrogen bonds. The remaining SAH-interacting residues are shown in (b). The 3HK-interacting residues via hydrogen bonds are shown in (c) and the remaining residues in (d). For comparison, the residues from the unbound structure are also shown in (c) and (d), with cyan carbons.
Figure 5
Figure 5
Proposed Ss-SibL C-methylation mechanism. Tyr134 and Tyr295 act as a tyrosine clamp to catalyze the transfer of methyl group from SAM to 3-HK.
See this image and copyright information in PMC

References

    1. Hurley L. H. & Gairola C. Pyrrolo (1,4) benzodiazepine antitumor antibiotics: Biosynthetic studies on the conversion of tryptophan to the anthranilic acid moieties of sibiromycin and tomaymycin. Antimicrob. Agents Chemother. 15, 42–45 (1979). - PMC - PubMed
    1. Hurley L. H. & Speedie M. K. Pyrrolo-(1,4)benzodiazepines antibiotics: Anthramycin, tomaymycin and sibiromycin. Springer, Berlin. 4 (1981). - PubMed
    1. Petrusek R. L. et al. Pyrrol[1,4]benzodiazepine antibiotics. Proposed structures and characteristics of the in vitro deoxyribonucleic acid adducts of anthramycin, tomaymycin, sibiromycin, and neothramycins A and B. Biochemistry 20, 1111–1119 (1981). - PubMed
    1. Gause G. F. Mechanism of Action of Antimicrobial and Antitumor Agents, Sibiromycin. Antibiotics 3, 269–273 (1975).
    1. Thurston D. E. et al. Effect of A-ring modifications on the DNA-binding behavior and cytotoxicity of pyrrolo[2,1-c][1,4]benzodiazepines. J. Med. Chem. 42, 1951–1964 (1999). - PubMed

Publication types

LinkOut - more resources