7UK8

Apo form of YgiC from Escherichia coli K-12

7UK8 の概要

• エントリーDOI: 10.2210/pdb7uk8/pdb
• 関連するPDBエントリー: 7UK6 7UK7
• 分子名称: Putative acid--amine ligase YgiC, NICKEL (II) ION, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: ligase, atp-grasp
• 由来する生物種: Escherichia coli K-12
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 46842.37

構造登録者

Pederick, J.L.,Bruning, J.B. (登録日: 2022-03-31, 公開日: 2023-02-15, 最終更新日: 2023-10-25)

主引用文献

Pederick, J.L.,Klose, J.,Jovcevski, B.,Pukala, T.L.,Bruning, J.B.
Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity.
Biochemistry, 62:899-911, 2023

PubMed Abstract: Polyamines and polyamine-containing metabolites are involved in many cellular processes related to bacterial cell growth and survival. In , the bifunctional enzyme glutathionylspermidine synthetase/amidase (GspSA) controls the production of glutathionylspermidine, which has a protective role against oxidative stress. also encodes two enzymes with homology to the synthetase domain of GspSA, YgiC, and YjfC; however, these do not catalyze the formation of glutathionylspermidine, and their catalytic function remained unknown. Here, we detail the structural and functional characterization of YgiC and YjfC. Using X-ray crystallography, the high-resolution crystal structures of YgiC and YjfC were obtained. This revealed that YgiC and YjfC possess multiple substitutions in key residues required for binding of glutathione in GspSA. Despite this difference, these enzymes share a similar active site structure to GspSA, suggesting that they catalyze the formation of an alternate peptide─spermidine conjugate. As the physiological substrates of YgiC and YjfC are unknown, this was probed using the peptide triglycine as a model substrate. A combination of enzyme activity assays and mass spectrometry revealed that YgiC and YjfC can function as peptide-spermidine ligases, forming a triglycine-spermidine conjugate. For both enzymes, conjugate formation was only observed in the presence of spermidine, but not other common polyamines, supporting that spermidine or a spermidine derivative is the physiological substrate. Importantly, since YgiC and YjfC are widely distributed in Gram-negative bacterial species, this suggests that these enzymes function in a conserved cellular process, representing a currently unknown aspect of bacterial polyamine metabolism.

PubMed: 36745518
DOI: 10.1021/acs.biochem.2c00592

実験手法

X-RAY DIFFRACTION (1.85 Å)