proteasome complex / proteasomal protein catabolic process / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)
AI070285
United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
AI088075
United States
Citation
Journal: J Biol Chem / Year: 2021 Title: The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome. Authors: Yanting Yin / Amanda Kovach / Hao-Chi Hsu / K Heran Darwin / Huilin Li / Abstract: Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. ...Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1-6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique β-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis-driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its β-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.
History
Deposition
Jan 29, 2021
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Header (metadata) release
May 5, 2021
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Map release
May 5, 2021
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Update
Mar 6, 2024
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Current status
Mar 6, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_23392.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate
Voxel size
X=Y=Z: 0.826 Å
Density
Contour Level
By AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum
-0.025549376 - 0.05442437
Average (Standard dev.)
0.0001871242 (±0.002086138)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
260
260
260
Spacing
260
260
260
Cell
A=B=C: 214.76 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.826
0.826
0.826
M x/y/z
260
260
260
origin x/y/z
0.000
0.000
0.000
length x/y/z
214.760
214.760
214.760
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
260
260
260
D min/max/mean
-0.026
0.054
0.000
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Supplemental data
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Sample components
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Entire : Cryo-EM structure of the Mpa hexamer in the presence of ATP and t...
Entire
Name: Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate
Components
Complex: Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate
Protein or peptide: AAA ATPase forming ring-shaped complexes
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE
Ligand: ADENOSINE-5'-DIPHOSPHATE
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Supramolecule #1: Cryo-EM structure of the Mpa hexamer in the presence of ATP and t...
Supramolecule
Name: Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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