The Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase Reveals an Ancient Fold for an Ancient Enzyme

Abstract

We report crystal structures of the citrate and sn-glycerol-1-phosphate (G1P) complexes of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Archaeoglobus fulgidus (AfGGGPS) at 1.55 and 2.0 Å resolution, respectively. AfGGGPS is an enzyme that performs the committed step in archaeal lipid biosynthesis, and it presents the first triose phosphate isomerase (TIM)-barrel structure with a prenyltransferase function. Our studies provide insight into the catalytic mechanism of AfGGGPS and demonstrate how it selects for the sn-G1P isomer. The replacement of "Helix 3" by a "strand" in AfGGGPS, a novel modification to the canonical TIMbarrel fold, suggests a model of enzyme adaptation that involves a "greasy slide" and a "swinging door." We propose functions for the homologous PcrB proteins, which are conserved in a subset of pathogenic bacteria, as either prenyltransferases or being involved in lipoteichoic acid biosynthesis. Sequence and structural comparisons lead us to postulate an early evolutionary history for AfGGGPS, which may highlight its role in the emergence of Archaea.The membrane lipids found in Archaea are a defining characteristic of this domain of life (1). These lipids are based on a core architecture where branched-chain saturated hydrocarbons are connected to glycerol through ether linkages (2, 3). In hyperthermophiles, two diphytanylglyceryl units are often linked covalently through their hydrocarbon tails to form tetraether lipids that completely span the membrane. In addition, archaeal membrane lipids have three general characteristics that distinguish them from their bacterial and eukaryotic counterparts (4). First, the phospholipid backbone is built upon the opposite glycerol stereoisomer, sn-glycerol-1-phosphate (G1P), 4 not the sn-glycerol-3-phosphate (G3P) backbone found in bacteria and eukaryotes. Second, the hydrophobic chains are isoprenoid derivatives instead of fatty acids. Third, the isoprenoid chains are bound to G1P through ether, not ester, linkages. Of these traits, the glycerol phosphate stereochemistry is the most distinctive because ether-linked lipids are known to exist in some eukaryotes and bacteria (5, 6), and phospholipid fatty acids have recently been described in Archaea (7). To date, however, there is no known exception to the G1P backbone stereochemistry of archaeal lipids or to the G3P backbone stereochemistry found in bacterial and eukaryotic lipids.The biosynthesis of archaeal membrane lipids is schematically illustrated in (Fig. 1). In brief, dimethylallyl diphosphate (DMAPP) and its isomer isopentenyl diphosphate are synthesized by a mevalonate-like pathway (2, 8). Long isoprenoid chains are produced from these fivecarbon precursors by consecutive condensations through the action of a prenyl diphosphate synthase. The committed step in archaeal lipid synthesis occurs with the formation of an ether linkage between G1P and an isoprenoid diphosphate, usually geranylgeranyl diphosphate (GGPP). Separate enzymes catalyze the sequential transfer of isoprenoid units onto ...

Biosynthesis of Ether-Type Polar Lipids in Archaea and Evolutionary Considerations

“…The pyrophosphate group attracts an electron pair of the carbon atom at the 1Ј position of the geranylgeranyl chain to give a partially positive charge, which attacks the glycerol oxygen. The crystal structure of GGGP synthase from Archaeoglobus fulgidus has been reported (88). It presents the first triose phosphate isomerase barrel structure with a prenyltransferase function.…”

“…GGPP synthase is involved in the formation of an ether bond by transferring an isoprenoid group to a nonlipid acceptor. The authors (88) emphasized that the evolutionary history of GGGP synthase reflects the emergence of archaea.…”

Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii

“…The crystal structure of the MfnF homolog in Methanococcus maripaludis, which was solved by A. P. Kuzin et al (PDB 3CET), exhibits a distinctive ␣/␤ two-layer sandwich structure (Fig. 7), unlike the ␣/␤ TIM barrel structure observed in thiamine synthase (32), dihydropteroate synthase (33,34), and GGGPS (31). In the active sites of both thiamine synthase and dihydropteroate synthase, the Mg 2ϩ used to stabilize the leaving pyrophosphate is ligated by two aspartic acid residues (33,35).…”

The molecular biology of moenomycins: towards novel antibiotics based on inhibition of bacterial peptidoglycan glycosyltransferases

“…In an unprecedented reaction in bacterial metabolism, enzyme MoeO5 controls the formation of the initial z-farnesyl-3-PG intermediate in MmA biosynthesis (Ostash et al, 2009). MoeO5 shows low homology to isoprenylglyceryl diphosphate synthases from Archaea, which couple either C 20 or C 25 isoprene chains to sn-glycerol-1-phosphate in the first dedicated step in the synthesis of Archaeal membrane lipids (Payandeh et al, 2006). z-farnesyl-3-PG serves as an acceptor substrate for the first Moe glycosyltransferase and, later in the pathway, a second prenylsynthase MoeN5.…”