5JJP

Crystal structure of CmiS6

Summary for 5JJP

• Entry DOI: 10.2210/pdb5jjp/pdb
• Related: 5JJQ
• Descriptor: Nonribosomal peptide synthase (2 entities in total)
• Functional Keywords: five-layered alpha-beta-alpha-beta-alpha sandwich fold, ligase, atp-binding
• Biological source: Streptomyces sp. MJ635-86F5
• Total number of polymer chains: 4
• Total formula weight: 234527.05

Authors

Cieslak, J.,Miyanaga, A.,Kudo, F.,Eguchi, T. (deposition date: 2016-04-25, release date: 2017-03-22, Last modification date: 2023-11-08)

Primary citation

Cieslak, J.,Miyanaga, A.,Takaku, R.,Takaishi, M.,Amagai, K.,Kudo, F.,Eguchi, T.
Biochemical characterization and structural insight into aliphatic beta-amino acid adenylation enzymes IdnL1 and CmiS6
Proteins, 85:1238-1247, 2017

PubMed Abstract: Macrolactam antibiotics such as incednine and cremimycin possess an aliphatic β-amino acid as a starter unit of their polyketide chain. In the biosynthesis of incednine and cremimycin, unique stand-alone adenylation enzymes IdnL1 and CmiS6 select and activate the proper aliphatic β-amino acid as a starter unit. In this study, we describe the enzymatic characterization and the structural basis of substrate specificity of IdnL1 and CmiS6. Functional analysis revealed that IdnL1 and CmiS6 recognize 3-aminobutanoic acid and 3-aminononanoic acid, respectively. We solved the X-ray crystal structures of IdnL1 and CmiS6 to understand the recognition mechanism of these aliphatic β-amino acids. These structures revealed that IdnL1 and CmiS6 share a common recognition motif that interacts with the β-amino group of the substrates. However, the hydrophobic side-chains of the substrates are accommodated differently in the two enzymes. IdnL1 has a bulky Leu220 located close to the terminal methyl group of 3-aminobutanoate of the trapped acyl-adenylate intermediate to construct a shallow substrate-binding pocket. In contrast, CmiS6 possesses Gly220 at the corresponding position to accommodate 3-aminononanoic acid. This structural observation was supported by a mutational study. Thus, the size of amino acid residue at the 220 position is critical for the selection of an aliphatic β-amino acid substrate in these adenylation enzymes. Proteins 2017; 85:1238-1247. © 2017 Wiley Periodicals, Inc.

PubMed: 28316096
DOI: 10.1002/prot.25284

Experimental method

X-RAY DIFFRACTION (2.3 Å)