Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniPathway vocabulary mapping
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Combined Automated Annotation using Multiple IEA Methods
Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria.
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PcrB is the heptaprenylglyceryl phosphate synthase of Bacillales, and its product is dephosphorylated and acetylated in the cell.
"PcrB, the bacterial homologue of the archaea-specific geranylgeranylglyceryl phosphate synthase, produces heptaprenylglyceryl phosphate in bacillales."
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The two processing steps that follow the PcrB reaction occur in vivo, so the ether lipid is a real cellular metabolite rather than an in vitro product.
"The product becomes dephosphorylated and acetylated in vivo."
A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization.
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Across seventeen characterized family members, the bacterial group I enzymes such as B. subtilis PcrB are heptaprenylglyceryl phosphate synthases, whereas the bacterial group II enzymes have archaeal-type geranylgeranylglyceryl phosphate synthase activity.
"differ from the bacterial group I enzymes that are heptaprenylglyceryl phosphate synthases"
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The reaction catalysed by the whole family is the formation of an ether bond between glycerol 1-phosphate and a polyprenyl diphosphate.
"family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates"
Two distinct mechanisms for TIM barrel prenyltransferases in bacteria.
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PcrB uses sn-glycerol 1-phosphate as its only acceptor, making it the first bacterial enzyme shown to use that enantiomer, and it transfers the prenyl group without isomerization so the trans-allylic geometry of the donor is retained.
"PcrB uses G1P (1) exclusively as an acceptor"
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The acceptor finding was framed as the first bacterial use of glycerol 1-phosphate as a substrate.
"making it the first known bacterial enzyme to use G1P as a substrate"
Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus.
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Mg2+ is required for catalysis, since no product forms in the presence of EDTA or in the absence of added magnesium.
"No product was found, indicating that Mg2+ is likely essential for catalysis."
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Crystal structures of B. subtilis and S. aureus PcrB, including complexes with glycerol 1-phosphate, define the acceptor site and the catalytic mechanism.
"PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate"
Dimerization determines substrate specificity of a bacterial prenyltransferase.
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Monomerized PcrB accepts only polyprenyl diphosphates of up to three isoprene units, so the homodimer is what allows the native seven-isoprene donor to be used, and quaternary structure is part of the chain-length specificity of the enzyme.
"activity assays showed that monomerization limits the length of accepted polyprenyl pyrophosphates to three isoprene units, whereas the native PcrB substrate contains seven isoprene entities"
Identification and Characterization of Heptaprenylglyceryl Phosphate Processing Enzymes in Bacillus subtilis.
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In Bacillales the PcrB product is not elaborated into an archaeal-type membrane lipid by addition of a second polyprenyl chain; it is dephosphorylated and acetylated instead, which is why the pathway output is a neutral ether lipid rather than a bulk phospholipid.
"In Bacillales, heptaprenylglyceryl phosphate does not become linked to a second polyprenyl moiety like ether lipids in Archaea but is dephosphorylated and acetylated."
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The dephosphorylating enzyme was enriched but never assigned to a gene; the acetyltransferase is YvoF, identified by screening a knock-out library.
"We enriched the phosphatase activity from a B. subtilis cell extract and suppose that dephosphorylation is catalyzed by the phosphatase PhoB or by any other phosphatase in an unspecific manner."
Lipoprotein N-terminal modification in Bacillus: a new paradigm for extracellular acetylation and species-dependent Toll-like receptor 2 immunomodulation.
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In B. subtilis, PcrB initiates synthesis of the lipophilic acetyl-carrier precursor; YvoF loads acetyl groups and LhaT performs transfer onto lipoprotein. This does not establish the same downstream use in every PcrB-containing lineage.
"PcrB condenses sn-glycerol 1-phosphate (G1P) with heptaprenyl pyrophosphate (HepPP) to form heptaprenylglyceryl phosphate (28, 29), which is subsequently dephosphorylated by a non-specific phosphatase prior to acetylation by YvoF to form acetylated heptaprenylglyceryl (Ac-HepG) with acetyl-coenzyme A (Ac-CoA) as donor (27)."
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Disruption of pcrB, yvoF or ypjA each abolishes lipoprotein N-acetylation, so all three are strictly required for the modification; back complementation restored it and the pathway was reconstituted in vitro from the four purified activities.
"Only pcrB, yvoF, and ypjA fully suppressed TLR2 activity, indicating these genes are strictly required for Ac-LP synthesis."
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The authors propose translocation of Ac-HepG to the extracytoplasmic lipoprotein acceptor used by LhaT; the transport mechanism is unidentified.
"The Ac-HepG extracellular acetyl donor is then shuttled across the membrane by an unidentified process where it is utilized by LhaT (YpjA)"
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The authors read the low abundance of HepG and Ac-HepG as evidence for a catalytic carrier role rather than a structural membrane-lipid role.
"A catalytic role as a transient carrier for acetyl groups, as opposed to being a structural membrane building block for an archeal-type lipid with ether-linked isoprenoid chains, is more consistent with the low overall abundance of HepG/Ac-HepG observed in B. subtilis membranes (28)."
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PcrB has a broader strain distribution than LhaT, leaving possible carrier functions outside the demonstrated Bacillus lipoprotein-acetylation pathway unresolved.
"The co-occurrence of PcrB with YpjA is not absolute, however, with PcrB enjoying a broader strain distribution than LhaT."
Identification and characterization of a bacterial glycerol-1-phosphate dehydrogenase: Ni(2+)-dependent AraM from Bacillus subtilis.
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AraM (EgsA) is a bacterial glycerol-1-phosphate dehydrogenase that reduces dihydroxyacetone phosphate to glycerol 1-phosphate, and was proposed to supply the glycerol 1-phosphate used for glycerolipid synthesis in Gram-positive bacteria. The proposal was not tested against heptaprenylglyceryl phosphate levels.
"we propose that AraM generates G1P for the synthesis of phosphoglycerolipids in Gram-positive bacterial species"
Guldan 2010 author dissertation: scoped EgsA kinetics and precursor-feeding evidence
Exact-term comparator and HAMAP scope adjudication for the PcrB ether-lipid proposal