5YGJ

Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.

(2018) ACS Catal 8: 4299-4312

• PubMed: 30345154 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1021/acscatal.8b00543
• Primary Citation of Related Structures:  
  5YGJ, 5YGK


• PubMed Abstract: 
  

  We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl ( S )-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold ( cis - head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg ²⁺ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg ²⁺ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H ⁺ , which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H ⁺ elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg ²⁺ can act as a general (imine-like) base, while Gln, Tyr and H ₂ O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H ₂ O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg ²⁺ , and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.

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Organizational Affiliation: 

Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.