Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies

Chang, Shuenn‐Yih; Ko, Tzu Ping; Chen, Annie P.-C.; Wang, Andrew H.J.; Liang, Po‐Huang

doi:10.1110/ps.03519904

Cited by 54 publications

(75 citation statements)

References 48 publications

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“…Medium-chain cis-PTs are represented by UPPS purified from a number of bacterial species (5,16,(23)(24)(25)(26)(27)(28)(29)(30), Z,E-mixed decaprenyl diphosphate synthase (Z,E-DecPP, C 50 ) from M. tuberculosis (Rv2361), as well as plant, protozoan, and archaeal enzymes. UPPS is responsible for the biogenesis of undecaprenyl phosphate, an indispensable glycosyl carrier lipid in bacterial cell wall biosynthesis.…”

Section: Classification Of Cis-ptsmentioning

confidence: 99%

cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases

Grabińska

Park

Sessa

2016

Journal of Biological Chemistry

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cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze consecutive condensation reactions of allylic diphosphate acceptor with isopentenyl diphosphate (IPP) in the cis (Z) configuration to generate linear polyprenyl diphosphate. The chain lengths of isoprenoid carbon skeletons vary widely from neryl pyrophosphate (C 10 ) to natural rubber (C >10,000 ). The homo-dimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS), has been structurally and mechanistically characterized in great detail and serves as a model for understanding the mode of action of eukaryotic cis-PTs. However, recent experiments have revealed that mammals, fungal, and long-chain plant cis-PTs are heteromeric enzymes composed of two distantly related subunits. In this review, the classification, function, and evolution of cis-PTs will be discussed with a special emphasis on the role of the newly described NgBR/Nus1 subunit and its plants' orthologs as essential, structural components of the cis-PTs activity.

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Section: Classification Of Cis-ptsmentioning

confidence: 99%

cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases

Grabińska

Park

Sessa

2016

Journal of Biological Chemistry

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“…6 B and C) (27,28,30). In Rv3378c, Asp34 sits in the expected position to carry out its essential catalytic function providing a specific mechanism that likely explains why mutant 1, which contains an Asp34→Gly alteration, does not (27,28,30) and the conserved location of Asp34 vis-à-vis the prenyl binding site (Fig. 6 A and B), mutation to asparagine or alanine abolished the prenyl transferase function of Rv3378c (SI Appendix, Fig.…”

Section: Rv3377c-rv3378cmentioning

confidence: 99%

“…6A). Although structural similarity was not predicted by sequence comparisons, Rv3378c adopts the fold seen in (Z)-prenyl or cis-prenyl transferases (27), including M. tuberculosis (Z)-farnesyl diphosphate synthase (Rv1086) and decaprenyl pyrophosphate synthase (Rv2361c), as well as Escherichia coli undecaprenyl pyrophosphate synthase (UPP) (28,29) (Fig. 6B).…”

Section: Rv3377c-rv3378cmentioning

confidence: 99%

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Molecular profiling ofMycobacterium tuberculosisidentifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c

Layre

Lee

Young

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

108

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To identify lipids with roles in tuberculosis disease, we systematically compared the lipid content of virulent Mycobacterium tuberculosis with the attenuated vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. Comparative lipidomics analysis identified more than 1,000 molecular differences, including a previously unknown, Mycobacterium tuberculosis-specific lipid that is composed of a diterpene unit linked to adenosine. We established the complete structure of the natural product as 1-tuberculosinyladenosine (1-TbAd) using mass spectrometry and NMR spectroscopy. A screen for 1-TbAd mutants, complementation studies, and gene transfer identified Rv3378c as necessary for 1-TbAd biosynthesis. Whereas Rv3378c was previously thought to function as a phosphatase, these studies establish its role as a tuberculosinyl transferase and suggest a revised biosynthetic pathway for the sequential action of Rv3377c-Rv3378c. In agreement with this model, recombinant Rv3378c protein produced 1-TbAd, and its crystal structure revealed a cis-prenyl transferase fold with hydrophobic residues for isoprenoid binding and a second binding pocket suitable for the nucleoside substrate. The dual-substrate pocket distinguishes Rv3378c from classical cis-prenyl transferases, providing a unique model for the prenylation of diverse metabolites. Terpene nucleosides are rare in nature, and 1-TbAd is known only in Mycobacterium tuberculosis. Thus, this intersection of nucleoside and terpene pathways likely arose late in the evolution of the Mycobacterium tuberculosis complex; 1-TbAd serves as an abundant chemical marker of Mycobacterium tuberculosis, and the extracellular export of this amphipathic molecule likely accounts for the known virulence-promoting effects of the Rv3378c enzyme.TbAd | terpenyl transferase W ith a mortality rate exceeding 1.5 million deaths annually, Mycobacterium tuberculosis remains one of the world's most important pathogens (1). M. tuberculosis succeeds as a pathogen because of productive infection of the endosomal network of phagocytes. Its residence within the phagosome protects it from immune responses during its decades long infection cycle. However, intracellular survival depends on active inhibition of pH-dependent killing mechanisms, which occurs for M. tuberculosis but not species with low disease-causing potential (2). Intracellular survival is also enhanced by an unusually hydrophobic and multilayered protective cell envelope. Despite study of this pathogen for more than a century, the spectrum of natural lipids within M. tuberculosis membranes is not yet fully defined. For example, the products of many genes annotated as lipid synthases remain unknown (3), and mass spectrometry detects hundreds of ions that do not correspond to known lipids in the MycoMass and LipidDB databases (4, 5).To broadly compare the lipid profiles of virulent and avirulent mycobacteria, we took advantage of a recently validated metabolomics platform (4). This high performance liquid chromatography-mass spectrometry (HPLC-MS)...

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“…UppS activity was also shown to be dependent on the presence of the divalent cation Mg 2 + for C 5 -PP binding and for catalysis, but not for initial C 15 -PP binding. 13,83 Several UppS three-dimensional (3D) structures, with 13,14,37 or without 29,59 bound substrates, were solved, which along with intensive mutagenesis 30,31,58 and kinetic studies 68,103 provided great knowledge on the functioning of this biosynthetic step. The condensation reaction catalyzed by prenyltransferases occurs via a nucleophilic attack of the C1-atom from the allylic substrate bearing the leaving phosphate group by the C4-atom of C 5 -PP (Fig.…”

Section: Synthesis Of Bacterial Undecaprenyl-diphosphatementioning

confidence: 99%

Deciphering the Metabolism of Undecaprenyl-Phosphate: The Bacterial Cell-Wall Unit Carrier at the Membrane Frontier

Manat

Roure

Auger

et al. 2014

Microbial Drug Resistance

121

139

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During the biogenesis of bacterial cell-wall polysaccharides, such as peptidoglycan, cytoplasmic synthesized precursors should be trafficked across the plasma membrane. This essential process requires a dedicated lipid, undecaprenyl-phosphate that is used as a glycan lipid carrier. The sugar is linked to the lipid carrier at the inner face of the membrane and is translocated toward the periplasm, where the glycan moiety is transferred to the growing polymer. Undecaprenyl-phosphate originates from the dephosphorylation of its precursor undecaprenyl-diphosphate, with itself generated by de novo synthesis or by recycling after the final glycan transfer. Undecaprenyl-diphosphate is de novo synthesized by the cytosolic cis-prenyltransferase undecaprenyldiphosphate synthase, which has been structurally and mechanistically characterized in great detail highlighting the condensation process. In contrast, the next step toward the formation of the lipid carrier, the dephosphorylation step, which has been overlooked for many years, has only started revealing surprising features. In contrast to the previous step, two unrelated families of integral membrane proteins exhibit undecaprenyldiphosphate phosphatase activity: BacA and members of the phosphatidic acid phosphatase type 2 super-family, raising the question of the significance of this multiplicity. Moreover, these enzymes establish an unexpected link between the synthesis of bacterial cell-wall polymers and other biological processes. In the present review, the current knowledge in the field of the bacterial lipid carrier, its mechanism of action, biogenesis, recycling, regulation, and future perspective works are presented.

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Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies

Cited by 54 publications

References 48 publications

cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases

cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases

Molecular profiling ofMycobacterium tuberculosisidentifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c

Deciphering the Metabolism of Undecaprenyl-Phosphate: The Bacterial Cell-Wall Unit Carrier at the Membrane Frontier

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