Structure and catalytic mechanism of a cyclic dipeptide prenyltransferase with broad substrate promiscuity.
Fungal indole prenyltransferases (PTs) typically act on specific substrates, and they are able to prenylate their target compounds with remarkably high regio- and stereoselectivity. Similar to several indole PTs characterized to date, the cyclic dipeptide N-prenyltransferase (CdpNPT) is able to prenylate a range of diverse substrates, thus exhibiting an unusually broad substrate promiscuity. To define the structural basis for this promiscuity, we have determined crystal structures of unliganded CdpNPT and of a ternary complex of CdpNPT bound to (S)-benzodiazepinedione and thiolodiphosphate. Analysis of the structures reveals a limited number of specific interactions with (S)-benzodiazepinedione, which projects into a largely hydrophobic surface. This surface can also accommodate other substrates, explaining the ability of the enzyme to prenylate a range of compounds. The location of the bound substrates suggests a likely reaction mechanism for the conversion of (S)-benzodiazepinedione. Structure-guided mutagenesis experiments confirm that, in addition to (S)-benzodiazepinedione, CdpNPT can also act on (R)-benzodiazepinedione and several cyclic dipeptides, albeit with relaxed specificity. Finally, nuclear magnetic resonance spectroscopy demonstrates that CdpNPT is a C-3 reverse PT that catalyzes the formation of C-3β prenylated indolines from diketopiperazines of tryptophan-containing cyclic dipeptides.
Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.
Jan Michael
JM
Schuller
Georg
G
Zocher
Mike
M
Liebhold
Xiulan
X
Xie
Mark
M
Stahl
Shu-Ming
SM
Li
Thilo
T
Stehle
D000595:Amino Acid Sequence; D001232:Aspergillus fumigatus / Q000201:enzymology; D002384:Catalysis; D018360:Crystallography, X-Ray; D004122:Dimethylallyltranstransferase / Q000737:chemistry* / Q000378:metabolism; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D007211:Indoles / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000737:chemistry / Q000378:metabolism; D054876:Prenylation; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014364:Tryptophan / Q000737:chemistry / Q000378:metabolism
D004151:Dipeptides; D005656:Fungal Proteins; D007211:Indoles; D010456:Peptides, Cyclic; C057812:indoline; D014364:Tryptophan; D004122:Dimethylallyltranstransferase