7UK8

Apo form of YgiC from Escherichia coli K-12

Summary for 7UK8

• Entry DOI: 10.2210/pdb7uk8/pdb
• Related: 7UK6 7UK7
• Descriptor: Putative acid--amine ligase YgiC, NICKEL (II) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: ligase, atp-grasp
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 1
• Total formula weight: 46842.37

Authors

Pederick, J.L.,Bruning, J.B. (deposition date: 2022-03-31, release date: 2023-02-15, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)