7N0J

Structure of YebY from E. coli K12

Summary for 7N0J

• Entry DOI: 10.2210/pdb7n0j/pdb
• Descriptor: YebY (2 entities in total)
• Functional Keywords: periplasmic protein, unknown function
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 12
• Total formula weight: 137552.09

Authors

Hadley, R.C.,Rosenzweig, A.C. (deposition date: 2021-05-25, release date: 2022-03-09, Last modification date: 2024-10-23)

Primary citation

Hadley, R.C.,Zhitnitsky, D.,Livnat-Levanon, N.,Masrati, G.,Vigonsky, E.,Rose, J.,Ben-Tal, N.,Rosenzweig, A.C.,Lewinson, O.
The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery.
J.Biol.Chem., 298:101445-101445, 2022

PubMed Abstract: The Escherichia coli yobA-yebZ-yebY (AZY) operon encodes the proteins YobA, YebZ, and YebY. YobA and YebZ are homologs of the CopC periplasmic copper-binding protein and the CopD putative copper importer, respectively, whereas YebY belongs to the uncharacterized Domain of Unknown Function 2511 family. Despite numerous studies of E. coli copper homeostasis and the existence of the AZY operon in a range of bacteria, the operon's proteins and their functional roles have not been explored. In this study, we present the first biochemical and functional studies of the AZY proteins. Biochemical characterization and structural modeling indicate that YobA binds a single Cu ion with high affinity. Bioinformatics analysis shows that YebY is widespread and encoded either in AZY operons or in other genetic contexts unrelated to copper homeostasis. We also determined the 1.8 Å resolution crystal structure of E. coli YebY, which closely resembles that of the lantibiotic self-resistance protein MlbQ. Two strictly conserved cysteine residues form a disulfide bond, consistent with the observed periplasmic localization of YebY. Upon treatment with reductants, YebY binds Cu and Cu with low affinity, as demonstrated by metal-binding analysis and tryptophan fluorescence. Finally, genetic manipulations show that the AZY operon is not involved in copper tolerance or antioxidant defense. Instead, YebY and YobA are required for the activity of the copper-related NADH dehydrogenase II. These results are consistent with a potential role of the AZY operon in copper delivery to membrane proteins.

PubMed: 34822841
DOI: 10.1016/j.jbc.2021.101445

Experimental method

X-RAY DIFFRACTION (1.88 Å)