Structural insights into the substrate binding sites of O-carbamoyltransferase VtdB from Streptomyces sp. NO1W98

De-Fa Rao; Hui Zhang; Ju-Ling Wang; Xiao-Xiao Meng; Zhen-Zhen Li; Chun-Ya Xie; Ikrame El Jaidi; Li Dai; Jing-Jing Ye; Min Zhu; Yu-Jie Peng; Qi Chen; Dao-Xiang Zhang; Yan-Bin Teng

doi:10.1016/j.bbrc.2023.03.081

Structural insights into the substrate binding sites of O-carbamoyltransferase VtdB from Streptomyces sp. NO1W98

Biochem Biophys Res Commun. 2023 Jun 4:659:40-45. doi: 10.1016/j.bbrc.2023.03.081. Epub 2023 Mar 31.

Authors

Affiliations

¹ School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China.
² School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China. Electronic address: zhangdaoxiang@ahmu.edu.cn.
³ School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China. Electronic address: tengyanbin@ahmu.edu.cn.

PMID: 37031593
DOI: 10.1016/j.bbrc.2023.03.081

Abstract

The O-carbamoyltransferase VtdB catalyzes the carbamoylation of venturicidin B, which is essential for the biosynthesis of the antibiotic venturicidin A. Here, the crystal structures of VtdB and VtdB in complex with the intermediate carbamoyladenylate (VtdB^CAO) were determined at resolutions of 2.99 Å and 2.90 Å, respectively. The structures resemble the conserved YrdC-like and specific Kae1-like domains. A magnesium ion and the intermediate carbamoyladenylate were also observed in the Kae1-like domain of VtdB. The structure of VtdB^CAO in complex with the substrate venturicidin B was modeled by a molecular docking method to better understand the substrate binding mode, revealing a novel venturicidin B binding pocket.

Keywords: Crystal structure; O-Carbamoyltransferase; Venturicidin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Crystallography, X-Ray
Molecular Docking Simulation
Streptomyces*
Substrate Specificity

Substances

3'-hydroxymethylcephem O-carbamoyltransferase
venturicidin B