8EFZ

Crystal structure of CcNikZ-II, apoprotein

8EFZ の概要

• エントリーDOI: 10.2210/pdb8efz/pdb
• 分子名称: Extracellular solute-binding protein family 5, CHLORIDE ION (3 entities in total)
• 機能のキーワード: nickel import, metal transport, abc-type transport, substrate binding protein, sbp protein, transport protein
• 由来する生物種: Clostridium carboxidivorans P7
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 113444.84

構造登録者

Stogios, P.J.,Evdokimova, E.,Diep, P.,Yakunin, A.,Mahadevan, K.,Savchenko, A. (登録日: 2022-09-10, 公開日: 2024-03-13, 最終更新日: 2025-03-26)

主引用文献

Diep, P.,Stogios, P.J.,Evdokimova, E.,Savchenko, A.,Mahadevan, R.,Yakunin, A.F.
Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies.
Febs J., 291:2980-2993, 2024

PubMed Abstract: Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

PubMed: 38555564
DOI: 10.1111/febs.17125

実験手法

X-RAY DIFFRACTION (2.38 Å)