9XIP

Structure of dodecameric Apo TpkB from Thermus thermophilus

Summary for 9XIP

• Entry DOI: 10.2210/pdb9xip/pdb
• EMDB information: 66911
• Descriptor: Serine protein kinase, ZINC ION (3 entities in total)
• Functional Keywords: hypothetical protein, atp-binding, prk/yeag family, structural genomics
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 12
• Total formula weight: 960512.80

Authors

Torri, M.,Kanno, R.,Mizoguchi, A.,Humbel, B.,Tani, K.,Masui, R. (deposition date: 2025-11-03, release date: 2026-07-01)

Primary citation

Torii, M.,Kanno, R.,Mizoguchi, A.,Humbel, B.M.,Tani, K.,Masui, R.
Structure and biochemical analyses suggest that PrkA/YeaG protein of Thermus thermophilus functions as a putative molecular chaperone.
J.Biochem., 2026

PubMed Abstract: Protein phosphorylation, a key post-translational modification, is mediated by various protein kinases. The bacterial PrkA/YeaG is recognized as an atypical protein kinase, but its activity remains elusive. This study investigated the structural and functional characteristics of a PrkA/YeaG homologue, TpkB, from Thermus thermophilus HB8. Using cryo-electron microscopy, the structures of TpkB in apo and AMPPNP-bound forms were determined, revealing a hexameric ring architecture characteristic of AAA + superfamily proteins. The TpkB protomer is comprised of an N-terminal domain, an ATPase domain, and a LID domain. The ATPase domain contains conserved sequence motifs associated with ATPase activity, whereas the other domains present a novel fold. TpkB exhibits structural similarity to MoxR family proteins, which possess chaperone-like functions in conjunction with von Willebrand factor A (vWA) domain proteins. Structural and gene neighborhood analyses suggested a functional link between PrkA/YeaG proteins and vWA domain proteins. Biochemical analyses demonstrated that TpkB exhibited ATPase activity and chaperone-like activity, but lacked detectable protein kinase activity. These findings establish TpkB as a novel member of the AAA+ superfamily with potential chaperone functions, providing new insights into the PrkA/YeaG family.

PubMed: 42294598
DOI: 10.1093/jb/mvag041

Experimental method

ELECTRON MICROSCOPY (2.3 Å)