## 1 Introduction  
With more than 80,000 molecules that have been discovered to date, terpenoids constitute one of the largest and most diverse groups in naturally occurring organic compounds [1]. These various chemicals are of significant interest to humans because of their extensive applications in the food, pharmaceutical, cosmetic, and agriculture industries. Despite their vast structural and functional diversity, terpenoids are de novo originated from two fundamental five-carbon (C5) precursors, namely, isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP) [2]. These C5 compounds are generated from one of two separate pathways: the mevalonate (MVA) pathway and the 2-C-methyl-d-erythitol 4-phosphate (MEP) pathway [3, 4]. Preryltransferases (PTs, also called isoprenyl diphosphate synthases, IDS) are the critical enzymes that subsequently condense DMAPP and IPP to polyprenyl pyrophosphates with various chain lengths. These series of polyprenyl pyrophosphates, including geranyl pyrophosphate (GPP, C10), famesyl pyrophosphate (FPP, C15), geranylgeranyl pyrophosphate (GGPP, C20), geranylfarmesyl pyrophosphate (GFPP, C25), and polyprenyl pyrophosphate with higher molecular weight, can be further catalyzed by a group of enzymes called terpene synthases (TPSs) to generate final products of monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), seaster terpenes (C25), and longer-chain-length terpenoids, respectively (Figure 1) [5; 6; 7]. Thus, prenyltransferases represent the first branch point and largely determine the terpenoid diversity. The PTs can be divided into two structurally and evolutionarily distinct classes as either _cis_- or _trans_-PTs according to the carbon-carbon double-bond configuration of the products, and the vast majority of terpenoids are derived from the products of _trans_-PTs [8]. According to the chain length of their predominant products, _trans_-PTs can be further classified as short-chain (_trans_-SC-PTs, C10-C25), medium-chain (_trans_-MC-PTs, C30-C35), and long-chain (_trans_-LC-PTs, C40-C50) PTs [9]. The catalytic mechanisms and protein structures of _trans_-PTs have been extensively explored in the previous studies: _trans_-PTs share a similar overall structure that 10 \(\alpha\) helices (A to J) form a large central cavity pocket with two conserved aspartate-rich motifs, DDx2-4D (the first aspartate-rich motif, FARM) and DDoxD (the second aspartate-rich motif, SARM) sited opposite in it. The condensation reactions occur in the cavity pocket, and the elongated polyprenyl groups scrunch into a product chain elongation tunnel constituted by \(\alpha\) helices D, E, and F (Figures 1 and S1) [9; 10]. The functional detection methods for _trans_-PTs are well established. The products can be either radioactively labeled and analyzed via chromatography or directly detected via HPLC-MS/MS [11; 12]. However, these methods are usually time-consuming and expensive, and they may need special permits. On the other hand, it is difficult to perform the functional annotations of uncharacterized _trans_-PTs sequences by simply using the  
Figure 1: The “three floors” model and scheme of terpenoid biosynthetic pathway. The “three floors” model is illustrated using AtGGPPS11. For clarity, a substrate FPP (magenta sticks) is modeled into the structure using 3 WJN as the reference model. The side-chains of residues from the “floors” are shown with sticks and colored in green (“first floor”), orange (“second floor”), and red (“third floor”). Dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP) from MVA/MEP pathways are used as substrates by _trans_-PTs to generate polyprenyl pyrophosphates with different chain lengths which are determined by the “three floors” model. These products from _trans_-PTs are the precursors of terpene synthases (TPSs) and can be further utilized to generate various terpenoids including sesquiterpenes (C15), diterpenes (C20), seasterterpenes (C25), and polyterpenes (\(\geq\)C30).