PDBsum entry 4lrd

Isomerase

PDB id: 4lrd

Contents

Protein chain

391 a.a.

Ligands

TRS

GOL ×2

Metals

_MN ×3

Waters ×305

PDB id:

4lrd

Name:

Isomerase

Title:

Phosphopentomutase 4h11 variant

Structure:

Phosphopentomutase 4h11 variant. Chain: a. Synonym: phosphodeoxyribomutase. Engineered: yes. Mutation: yes

Source:

Bacillus cereus. Organism_taxid: 1396. Gene: bc_4087, deob. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.78Å R-factor: 0.142 R-free: 0.180

Authors:

W.A.Birmingham,C.A.Starbird,T.D.Panosian,D.P.Nannemann,T.M.Iverson, B.O.Bachmann

Key ref:

W.R.Birmingham et al. (2014). Bioretrosynthetic construction of a didanosine biosynthetic pathway. Nat Chem Biol, 10, 392-399. PubMed id: 24657930 DOI: 10.1038/nchembio.1494

Date:

19-Jul-13 Release date: 31-Jul-13

Protein chain

Q818Z9  (DEOB_BACCR) -  Phosphopentomutase from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)

Seq: 394 a.a.

Struc: 391 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.4.2.7 - phosphopentomutase.
• Reaction: alpha-D-ribose 1-phosphate = D-ribose 5-phosphate

alpha-D-ribose 1-phosphate (Bound ligand (Het Group name = GOL) matches with 42.86% similarity) = D-ribose 5-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/nchembio.1494

Nat Chem Biol 10:392-399 (2014)

PubMed id: 24657930

Bioretrosynthetic construction of a didanosine biosynthetic pathway.

W.R.Birmingham, C.A.Starbird, T.D.Panosian, D.P.Nannemann, T.M.Iverson, B.O.Bachmann.

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.