4LRA

Phosphopentomutase S154G variant

Summary for 4LRA

• Entry DOI: 10.2210/pdb4lra/pdb
• Related: 3M8Z 3TWZ 3TX0 3UN3 4LR7 4LR8 4LR9 4LRB 4LRC 4LRD 4LRE 4LRF
• Descriptor: Phosphopentomutase, MANGANESE (II) ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: alkaline phosphatase family, isomerase
• Biological source: Bacillus cereus
• Total number of polymer chains: 3
• Total formula weight: 140029.67

Authors

Birmingham, W.A.,Starbird, C.A.,Panosian, T.D.,Nannemann, D.P.,Iverson, T.M.,Bachmann, B.O. (deposition date: 2013-07-19, release date: 2013-07-31, Last modification date: 2023-09-20)

Primary citation

Birmingham, W.R.,Starbird, C.A.,Panosian, T.D.,Nannemann, D.P.,Iverson, T.M.,Bachmann, B.O.
Bioretrosynthetic construction of a didanosine biosynthetic pathway.
Nat.Chem.Biol., 10:392-399, 2014

PubMed Abstract: Concatenation of engineered biocatalysts into multistep pathways markedly increases their utility, but the development of generalizable assembly methods remains a major challenge. Herein we evaluate 'bioretrosynthesis', which is an application of the retrograde evolution hypothesis, for biosynthetic pathway construction. To test bioretrosynthesis, we engineered a pathway for synthesis of the antiretroviral nucleoside analog didanosine (2',3'-dideoxyinosine). Applying both directed evolution- and structure-based approaches, we began pathway construction with a retro-extension from an engineered purine nucleoside phosphorylase and evolved 1,5-phosphopentomutase to accept the substrate 2,3-dideoxyribose 5-phosphate with a 700-fold change in substrate selectivity and threefold increased turnover in cell lysate. A subsequent retrograde pathway extension, via ribokinase engineering, resulted in a didanosine pathway with a 9,500-fold change in nucleoside production selectivity and 50-fold increase in didanosine production. Unexpectedly, the result of this bioretrosynthetic step was not a retro-extension from phosphopentomutase but rather the discovery of a fortuitous pathway-shortening bypass via the engineered ribokinase.

PubMed: 24657930
DOI: 10.1038/nchembio.1494

Experimental method

X-RAY DIFFRACTION (2 Å)