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

Wanda Gillon,Masahiro Fujihashi,Jian Payandeh,Emil F Pai

doi:10.1074/jbc.m509377200

Wanda Gillon, Masahiro Fujihashi + Show 2 more

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https://doi.org/10.1074/jbc.m509377200

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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 A 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 TIM-barrel 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.

Highlights

Stereoisomer, sn-glycerol-1-phosphate (G1P),4 not the sn-glycerol-3phosphate (G3P) backbone found in bacteria and eukaryotes
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)
The Group I geranylgeranylglyceryl phosphate synthase (GGGPS) from A. fulgidus (AfGGGPS) presents a dimeric structure (Fig. 2, B and C)

Summary

Structure of Geranylgeranylglyceryl Phosphate Synthase

Gram-positive bacteria, including the human pathogens Bacillus anthracis, Staphylococcus aureus, and Listeria monocytogenes [8, 12, 15]. To gain more insight into the unique stereochemistry of the unusual reaction catalyzed by GGGPS, and to shed light onto the function of PcrB, we have determined crystal structures of GGGPS from the sulfatereducing hyperthermophile Archaeoglobus fulgidus in complex with G1P and citrate. The present work reveals 1) an ancient fold for this deeply rooted enzyme and 2) establishes, for the first time, a prenyltransferase function on a TIM-barrel scaffold. Our structures further unveil 3) how the “standard phosphate-binding motif” is utilized in concert with conserved active site residues to select for the G1P substrate, 4) a long apolar cavity that bears the hallmarks of a hydrocarbon ruler, and 5) a unique change to the classical (␤␣)8-TIM-barrel fold, which prompts us to present a hypothesis for the functional consequences of this adaptation

MATERIALS AND METHODS

RESULTS AND DISCUSSION

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