Reaction participants Show >> << Hide
- Name help_outline gentamicin X2 Identifier CHEBI:195255 Charge 4 Formula C19H42N4O10 InChIKeyhelp_outline HFLKNINDVFJPQT-ZFAMMYHGSA-R SMILEShelp_outline C1[C@]([C@@H]([C@H]([C@H](O1)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@H]3O[C@@H]([C@H]([C@@H]([C@H]3[NH3+])O)O)CO)[NH3+])[NH3+])O)[NH2+]C)(C)O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline methylcob(III)alamin Identifier CHEBI:28115 (CAS: 13422-55-4) help_outline Charge 0 Formula C63H91CoN13O14P InChIKeyhelp_outline JEWJRMKHSMTXPP-WZHZPDAFSA-L SMILEShelp_outline [H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)n4c[n+](c5cc(C)c(C)cc45)[Co-3]456(C)N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O 2D coordinates Mol file for the small molecule Search links Involved in 9 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline S-adenosyl-L-methionine Identifier CHEBI:59789 Charge 1 Formula C15H23N6O5S InChIKeyhelp_outline MEFKEPWMEQBLKI-AIRLBKTGSA-O SMILEShelp_outline C[S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 938 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline geneticin Identifier CHEBI:195256 Charge 4 Formula C20H44N4O10 InChIKeyhelp_outline BRZYSWJRSDMWLG-CAXSIQPQSA-R SMILEShelp_outline C1[C@]([C@@H]([C@H]([C@H](O1)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@H]3O[C@@H]([C@H]([C@@H]([C@H]3[NH3+])O)O)C(O)C)[NH3+])[NH3+])O)[NH2+]C)(C)O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline cob(III)alamin Identifier CHEBI:28911 (CAS: 13408-78-1) help_outline Charge 1 Formula C62H88CoN13O14P InChIKeyhelp_outline NSLAUEAQDBERRV-DSRCUDDDSA-L SMILEShelp_outline [H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)n4c[n+](c5cc(C)c(C)cc45)[Co--]456N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O 2D coordinates Mol file for the small molecule Search links Involved in 6 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline 5'-deoxyadenosine Identifier CHEBI:17319 (CAS: 4754-39-6) help_outline Charge 0 Formula C10H13N5O3 InChIKeyhelp_outline XGYIMTFOTBMPFP-KQYNXXCUSA-N SMILEShelp_outline C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 76 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline L-methionine Identifier CHEBI:57844 Charge 0 Formula C5H11NO2S InChIKeyhelp_outline FFEARJCKVFRZRR-BYPYZUCNSA-N SMILEShelp_outline CSCC[C@H]([NH3+])C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 131 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
| RHEA:77223 | RHEA:77224 | RHEA:77225 | RHEA:77226 | |
|---|---|---|---|---|
| Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
| UniProtKB help_outline |
|
|||
| KEGG help_outline | ||||
| MetaCyc help_outline |
Publications
-
Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration.
Kim H.J., Liu Y.N., McCarty R.M., Liu H.W.
Many cobalamin (Cbl)-dependent radical S-adenosyl-l-methionine (SAM) methyltransferases have been identified through sequence alignment and/or genetic analysis; however, few have been studied in vitro. GenK is one such enzyme that catalyzes methylation of the 6'-carbon of gentamicin X<sub>2</sub> ... >> More
Many cobalamin (Cbl)-dependent radical S-adenosyl-l-methionine (SAM) methyltransferases have been identified through sequence alignment and/or genetic analysis; however, few have been studied in vitro. GenK is one such enzyme that catalyzes methylation of the 6'-carbon of gentamicin X<sub>2</sub> (GenX<sub>2</sub>) to produce G418 during the biosynthesis of gentamicins. Reported herein, several alternative substrates and fluorinated substrate analogs were prepared to investigate the mechanism of methyl transfer from Cbl to the substrate as well as the substrate specificity of GenK. Experiments with deuterated substrates are also shown here to demonstrate that the 6'-pro-R-hydrogen atom of GenX<sub>2</sub> is stereoselectively abstracted by the 5'-dAdo· radical and that methylation occurs with retention of configuration at C6'. Based on these observations, a model of GenK catalysis is proposed wherein free rotation of the radical-bearing carbon is prevented and the radical SAM machinery sits adjacent rather than opposite to the Me-Cbl cofactor with respect to the substrate in the enzyme active site. << Less
J Am Chem Soc 139:16084-16087(2017) [PubMed] [EuropePMC]
This publication is cited by 3 other entries.
-
Studies of GenK and OxsB, two B<sub>12</sub>-dependent radical SAM enzymes involved in natural product biosynthesis.
Lee Y.H., Liu H.W.
The B<sub>12</sub>-dependent radical SAM enzymes are an emerging subgroup of biological catalysts that bind a cobalamin cofactor in addition to the canonical [Fe<sub>4</sub>S<sub>4</sub>] cluster characteristic of radical SAM enzymes. Most of the B<sub>12</sub>-dependent radical SAM enzymes that h ... >> More
The B<sub>12</sub>-dependent radical SAM enzymes are an emerging subgroup of biological catalysts that bind a cobalamin cofactor in addition to the canonical [Fe<sub>4</sub>S<sub>4</sub>] cluster characteristic of radical SAM enzymes. Most of the B<sub>12</sub>-dependent radical SAM enzymes that have been characterized mediated methyltransfer reactions; however, a small number are known to catalyze more diverse reactions such as ring contractions. Thus, Genk is a methyltransferase from the gentamicin C biosynthetic pathway, whereas OxsB catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphates to generate an oxetane aldehyde during the biosynthesis of oxetanocin A. The preparation and in vitro characterization of such enzymes is complicated by the presence of two redox sensitive cofactors in addition to challenges in obtaining soluble protein for study. This chapter describes expression, purification and assay methodologies for GenK and OxsB highlighting the use of denaturation/refolding protocols for solubilizing inclusion bodies as well as the use of cluster assembly and cobalamin uptake machinery during in vivo expression. << Less
Methods Enzymol 669:71-90(2022) [PubMed] [EuropePMC]
This publication is cited by 3 other entries.
-
GenK-catalyzed C-6' methylation in the biosynthesis of gentamicin: isolation and characterization of a cobalamin-dependent radical SAM enzyme.
Kim H.J., McCarty R.M., Ogasawara Y., Liu Y.N., Mansoorabadi S.O., LeVieux J., Liu H.W.
The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-l-methionine (SAM) superfamily was previously predicted on the basis of bioinformatic analysis. A number of these are Cbl-dependent methyltransferases, but the details surrounding their reaction mechanism ... >> More
The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-l-methionine (SAM) superfamily was previously predicted on the basis of bioinformatic analysis. A number of these are Cbl-dependent methyltransferases, but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp(3) carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that 1 equiv each of 5'-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. On the basis of these results, one mechanistic possibility for the GenK reaction can be ruled out, and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed. << Less
J Am Chem Soc 135:8093-8096(2013) [PubMed] [EuropePMC]
This publication is cited by 3 other entries.
Comments
RHEA:77223 part of RHEA:77227