7DQ5

Crystal structure of HitB in complex with (S)-beta-phenylalanine sulfamoyladenosine

Summary for 7DQ5

• Entry DOI: 10.2210/pdb7dq5/pdb
• Descriptor: Putative ATP-dependent b-aminoacyl-ACP synthetase, [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-phenyl-propanoyl]sulfamate, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: hitachimycin, polyketide biosynthesis, atp binding, adenylation, ligase
• Biological source: Embleya scabrispora
• Total number of polymer chains: 2
• Total formula weight: 120416.53

Authors

Kudo, F.,Takahashi, S.,Miyanaga, A.,Nakazawa, Y.,Eguchi, T. (deposition date: 2020-12-22, release date: 2021-03-03, Last modification date: 2023-11-29)

Primary citation

Kudo, F.,Takahashi, S.,Miyanaga, A.,Nakazawa, Y.,Nishino, K.,Hayakawa, Y.,Kawamura, K.,Ishikawa, F.,Tanabe, G.,Iwai, N.,Nagumo, Y.,Usui, T.,Eguchi, T.
Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB.
Acs Chem.Biol., 16:539-547, 2021

PubMed Abstract: Hitachimycin is a macrolactam antibiotic with an ()-β-phenylalanine (β-Phe) at the starter position of its polyketide skeleton. ()-β-Phe is formed from l-α-phenylalanine by the phenylananine-2,3-aminomutase HitA in the hitachimycin biosynthetic pathway. In this study, we produced new hitachimycin analogs via mutasynthesis by feeding various ()-β-Phe analogs to a Δ strain. We obtained six hitachimycin analogs with F at the , , or position and Cl, Br, or a CH group at the position of the phenyl moiety, as well as two hitachimycin analogs with thienyl substitutions. Furthermore, we carried out a biochemical and structural analysis of HitB, a β-amino acid-selective adenylation enzyme that introduces ()-β-Phe into the hitachimycin biosynthetic pathway. The values of the incorporated ()-β-Phe analogs and natural ()-β-Phe were similar. However, the values of unincorporated ()-β-Phe analogs with Br and a CH group at the or position of the phenyl moiety were high, indicating that HitB functions as a gatekeeper to select macrolactam starter units during mutasynthesis. The crystal structure of HitB in complex with ()-β-3-Br-phenylalanine sulfamoyladenosine (β--Br-Phe-SA) revealed that the bulky Br group is accommodated by the conformational flexibility around Phe328, whose side chain is close to the position. The aromatic group of β--Br-Phe-SA is surrounded by hydrophobic and aromatic residues, which appears to confer the conformational flexibility that enables HitB to accommodate the -substituted ()-β-Phe. The new hitachimycin analogs exhibited different levels of biological activity in HeLa cells and multidrug-sensitive budding yeast, suggesting that they may target different molecules.

PubMed: 33625847
DOI: 10.1021/acschembio.1c00003

Experimental method

X-RAY DIFFRACTION (2.45 Å)