5UFN

Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound S-adenosylhomocysteine

Summary for 5UFN

• Entry DOI: 10.2210/pdb5ufn/pdb
• Related: 5UFM
• Descriptor: Methyltransferase domain protein, S-ADENOSYL-L-HOMOCYSTEINE, SULFATE ION, ... (5 entities in total)
• Functional Keywords: transferase, n-methyltransferase, complex, s-adenosylmethionine-dependent
• Biological source: Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
• Total number of polymer chains: 2
• Total formula weight: 54983.02

Authors

Fenwick, M.K.,Ealick, S.E.,Almabruk, K.H.,Begley, T.P.,Philmus, B. (deposition date: 2017-01-05, release date: 2017-12-13, Last modification date: 2024-03-06)

Primary citation

Fenwick, M.K.,Almabruk, K.H.,Ealick, S.E.,Begley, T.P.,Philmus, B.
Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase.
Biochemistry, 56:3934-3944, 2017

PubMed Abstract: Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp orbital of N6 and then toward an sp orbital of N1 after planar rotation of the azapteridine ring system. Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.

PubMed: 28665591
DOI: 10.1021/acs.biochem.7b00476

Experimental method

X-RAY DIFFRACTION (1.39 Å)