PDBsum entry 6itd

Oxidoreductase

PDB id: 6itd

Contents

Protein chain

328 a.a.

Ligands

IKT

Waters ×49

PDB id:

6itd

Name:

Oxidoreductase

Title:

Crystal structure of biou (k124a) from synechocystis sp.Pcc6803 in complex with the analog of reaction intermediate, 3-(1-aminoethyl)- nonanedioic acid

Structure:

Slr0355 protein. Chain: a. Synonym: biou. Engineered: yes. Mutation: yes

Source:

Synechocystis sp. Pcc 6803. Organism_taxid: 1148. Gene: slr0355. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.190 R-free: 0.249

Authors:

K.Sakaki,T.Tomita,T.Kuzuyama,M.Nishiyama

Key ref:

K.Sakaki et al. (2020). A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol, 16, 415-422. PubMed id: 32042199 DOI: 10.1038/s41589-019-0461-9

Date:

21-Nov-18 Release date: 15-Jan-20

Protein chain

Q55650  (Q55650_SYNY3) -  (S)-8-amino-7-oxononanoate synthase BioU from Synechocystis sp. (strain PCC 6803 / Kazusa)

Seq: 331 a.a.

Struc: 328 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.6.1.121 - 8-amino-7-oxononanoate carboxylating dehydrogenase.
• Reaction: (8S)-8-amino-7-oxononanoate + L-lysyl-[protein] + CO2 = (S)-2-amino-6- oxohexanoyl-[protein] + (7R,8S)-8-amino-7-(carboxyamino)nonanoate + 2 H⁺

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

Key reference

DOI no: 10.1038/s41589-019-0461-9

Nat Chem Biol 16:415-422 (2020)

PubMed id: 32042199

A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.

K.Sakaki, K.Ohishi, T.Shimizu, I.Kobayashi, N.Mori, K.Matsuda, T.Tomita, H.Watanabe, K.Tanaka, T.Kuzuyama, M.Nishiyama.

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.