5Y4C

Crystal structure of EfeO-like protein Algp7 in complex with a metal ion

Summary for 5Y4C

• Entry DOI: 10.2210/pdb5y4c/pdb
• Descriptor: Alginate-binding protein, GLYCEROL, COPPER (II) ION, ... (4 entities in total)
• Functional Keywords: two up-and-down four-helical bundles, alginate binding, metal binding, structural protein
• Biological source: Sphingomonas sp. A1
• Total number of polymer chains: 1
• Total formula weight: 31856.73

Authors

Temtrirath, K.,Maruyama, Y.,Mikami, B.,Murata, K.,Hashimoto, W. (deposition date: 2017-08-03, release date: 2017-10-04, Last modification date: 2023-11-22)

Primary citation

Temtrirath, K.,Okumura, K.,Maruyama, Y.,Mikami, B.,Murata, K.,Hashimoto, W.
Binding mode of metal ions to the bacterial iron import protein EfeO
Biochem. Biophys. Res. Commun., 493:1095-1101, 2017

PubMed Abstract: The tripartite EfeUOB system functions as a low pH iron importer in Gram-negative bacteria. In the alginate-assimilating bacterium Sphingomonas sp. strain A1, an additional EfeO-like protein (Algp7) is encoded downstream of the efeUOB operon. Here we show the metal binding mode of Algp7, which carries a M_75 metallopeptidase motif. The Algp7 protein was purified from recombinant E. coli cells and was subsequently characterized using differential scanning fluorimetry, fluorescence spectrometry, atomic absorption spectroscopy, and X-ray crystallography. The fluorescence of a dye, SYPRO Orange, bound to denatured Algp7 in the absence and presence of metal ions was measured during heat treatment. The fluorescence profile of Algp7 in the presence of metals such as ferric, ferrous, and zinc ions, shifted to a higher temperature, suggesting that Algp7 binds these metal ions and that metal ion-bound Algp7 is more thermally stable than the ligand-free form. Algp7 was directly demonstrated to show an ability to bind copper ion by atomic absorption spectroscopy. Crystal structure of metal ion-bound Algp7 revealed that the metal ion is bound to the cleft surrounded by several acidic residues. Four residues, Glu79, Glu82, Asp96, and Glu178, distinct from the M_75 motif (His115xxGlu118), are coordinated to the metal ion. This is the first report to provide structural insights into metal binding by the bacterial EfeO element.

PubMed: 28919419
DOI: 10.1016/j.bbrc.2017.09.057

Experimental method

X-RAY DIFFRACTION (2.701 Å)