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TitleATP hydrolysis-coupled peptide translocation mechanism of ClpB.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 115, Issue 41, Page E9560-E9569, Year 2018
Publish dateOct 9, 2018
AuthorsHongjun Yu / Tania J Lupoli / Amanda Kovach / Xing Meng / Gongpu Zhao / Carl F Nathan / Huilin Li /
PubMed AbstractThe protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In (), ClpB facilitates asymmetric distribution ...The protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In (), ClpB facilitates asymmetric distribution of protein aggregates during cell division to help the pathogen survive and persist within the host, but a mechanistic understanding has been lacking. Here we report cryo-EM structures at 3.8- to 3.9-Å resolution of ClpB bound to a model substrate, casein, in the presence of the weakly hydrolyzable ATP mimic adenosine 5'-[γ-thio]triphosphate. ClpB existed in solution in two closed-ring conformations, conformers 1 and 2. In both conformers, the 12 pore-loops on the 12 NTDs of the six protomers (P1-P6) were arranged similarly to a staircase around the bound peptide. Conformer 1 is a low-affinity state in which three of the 12 pore-loops (the protomer P1 NBD1 and NBD2 loops and the protomer P2 NBD1 loop) are not engaged with peptide. Conformer 2 is a high-affinity state because only one pore-loop (the protomer P2 NBD1 loop) is not engaged with the peptide. The resolution of the two conformations, along with their bound substrate peptides and nucleotides, enabled us to propose a nucleotide-driven peptide translocation mechanism of a bacterial ClpB that is largely consistent with several recent unfoldase structures, in particular with the eukaryotic Hsp104. However, whereas Hsp104's two NBDs move in opposing directions during one step of peptide translocation, in Mtb ClpB the two NBDs move only in the direction of translocation.
External linksProc Natl Acad Sci U S A / PubMed:30257943 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 6.3 Å
Structure data

7942

6dju

EMDB-7942, PDB-6dju:
Mtb ClpB in complex with ATPgammaS and casein, Conformer 1
Method: EM (single particle) / Resolution: 3.8 Å

7943

6djv

EMDB-7943, PDB-6djv:
Mtb ClpB in complex with ATPgammaS and casein, Conformer 2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-9027:
Mtb ClpB in complex with ATPgammaS and casein, Combined
Method: EM (single particle) / Resolution: 3.6 Å

9028

6ed3

EMDB-9028, PDB-6ed3:
Mtb ClpB in complex with AMPPNP
Method: EM (single particle) / Resolution: 6.3 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

Source
  • mycobacterium tuberculosis (bacteria)
  • bos taurus (cattle)
KeywordsCHAPERONE / cryoEM / pathogen / AAA ATPase / Mycobacterium tuberculosis / unfoldase

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