8YOZ

Crystal structure of the small zinc-finger protein ZifS (TTHA0897) from Thermus thermophilus HB8.

Summary for 8YOZ

• Entry DOI: 10.2210/pdb8yoz/pdb
• Descriptor: Transcription factor zinc-finger domain-containing protein, ZINC ION (3 entities in total)
• Functional Keywords: zinc finger, unknown function
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 2
• Total formula weight: 19473.41

Authors

Kurinami, S.,Fukui, K.,Murakawa, T.,Baba, S.,Kumasaka, T.,Okanishi, H.,Kanai, Y.,Yano, T.,Masui, R. (deposition date: 2024-03-14, release date: 2025-03-19, Last modification date: 2025-06-11)

Primary citation

Kurinami, S.,Fukui, K.,Murakawa, T.,Baba, S.,Kumasaka, T.,Okanishi, H.,Kanai, Y.,Yano, T.,Masui, R.
The crystal structure of the small zinc-finger protein ZifS from Thermus thermophilus HB8.
J.Biochem., 2025

PubMed Abstract: Zinc finger domains are important interaction modules for binding to nucleic acids, proteins, lipids, and small molecules. Many small-sized zinc finger proteins are encoded in bacterial genomes, but most of them have not been functionally annotated. We focused on TTHA0897, ZifS, as a small zinc finger protein from the extremely thermophilic eubacterium Thermus thermophilus HB8. In vivo experiments suggested that the cellular function of ZifS is related to the growth transition of T. thermophilus from the lag to the exponential phase under nutritionally limited conditions. In vitro biochemical experiments, including electrophoretic mobility shift assay and pull-down assay, yielded no clues about molecular functions of ZifS. X-ray crystallographic analysis revealed that the dimeric ZifS globally forms a cylinder-like structure, although ZifS dimer has no overall structural similarity to other known zinc finger proteins. The zinc ion-binding manner of ZifS fitted the characteristics of the zinc ribbon fold, which are mostly found in domains from proteins involved in the transcriptional and translational machinery. The crystal structure of ZifS is the first experimental insight into the molecular structure of this protein family, revealing several conserved features that may be functionally relevant.

PubMed: 40441711
DOI: 10.1093/jb/mvaf028

Experimental method

X-RAY DIFFRACTION (1.83 Å)