6ITD

Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid

Summary for 6ITD

• Entry DOI: 10.2210/pdb6itd/pdb
• Descriptor: Slr0355 protein, 3-(1-AMINOETHYL)NONANEDIOIC ACID (3 entities in total)
• Functional Keywords: biou, biotin biosynthesis, synechocystis, oxidoreductase
• Biological source: Synechocystis sp. PCC 6803
• Total number of polymer chains: 1
• Total formula weight: 38026.08

Authors

Sakaki, K.,Tomita, T.,Kuzuyama, T.,Nishiyama, M. (deposition date: 2018-11-21, release date: 2020-01-15, Last modification date: 2023-11-22)

Primary citation

Sakaki, K.,Ohishi, K.,Shimizu, T.,Kobayashi, I.,Mori, N.,Matsuda, K.,Tomita, T.,Watanabe, H.,Tanaka, K.,Kuzuyama, T.,Nishiyama, M.
A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Nat.Chem.Biol., 16:415-422, 2020

PubMed Abstract: In biotin biosynthesis, the conversion of pimeloyl intermediates to biotin is catalyzed by a universal set of four enzymes: BioF, BioA, BioD and BioB. We found that the gene homologous to bioA, the product of which is involved in the conversion of 8-amino-7-oxononanoate (AON) to 7,8-diaminononanoate (DAN), is missing in the genome of the cyanobacterium Synechocystis sp. PCC 6803. We provide structural and biochemical evidence showing that a novel dehydrogenase, BioU, is involved in biotin biosynthesis and functionally replaces BioA. This enzyme catalyzes three reactions: formation of covalent linkage with AON to yield a BioU-DAN conjugate at the ε-amino group of Lys124 of BioU using NAD(P)H, carboxylation of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-carbamic acid using NAD(P). In this biosynthetic pathway, BioU is a suicide enzyme that loses the Lys124 amino group after a single round of reaction.

PubMed: 32042199
DOI: 10.1038/s41589-019-0461-9

Experimental method

X-RAY DIFFRACTION (2 Å)