1. Volume 24, Issue 5, Pages 667-675 (May 2016)
Structural Insights into the Allosteric Operation of the Lon AAA+ Protease 
Chien-Chu Lin, Shih-Chieh Su, Ming-Yuan Su, Pi-Hui Liang, Chia-Cheng Feng, Shih-Hsiung Wu, Chung-I Chang 
Structure 
Volume 24, Issue 5, Pages (May 2016)
DOI: /j.str
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2. Structure 2016 24, 667-675DOI: (10.1016/j.str.2016.03.001)
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3. Figure 1 Overall Structure of the Core-E423Q Complex
(A) Domain organization of MtaLonA and cartoon diagram illustrating the assembly of Core-E423Q bound to three ADPs. The asterisk indicates the point mutation. The letters A to F are PDB chain identifiers. The white dotted circles denote unoccupied ATPase sites.
(B) Two orthogonal views of the Core-E423Q complex.
(C) Side view of the Core-E423Q complex, in semi-transparent surface, showing a significant conformational difference between ADP-bound protomer B and nucleotide-free protomer E shown as ribbons. MMH8709 is shown as spheres. The pore loop, loop 2, sensor I, and the β10-β11 hairpin are marked by orange, green, black, and magenta symbols, respectively. The nucleotide-free and ADP-bound protomers are colored in blue and gold, respectively.
See also the NA492 structure, sequence alignment, and the structures of bound ADPs in Figures S1–S3.
Structure  , DOI: ( /j.str )
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4. Figure 2 ADP-Induced Conformational Changes in the LonA Protomers
(A) Stereo view of the structures of the nucleotide (NTD)-free protomer A (blue) and ADP-bound protomer B (gold) superimposed based on the protease domain. The pore-loop residue Y397, loop-2 residue W431, and the sensor-I N471 are labeled and shown in spheres. The β10-β11 hairpins are highlighted in magenta.
(B) Superimposed structures of the six α/β domains showing the variable pore-loop and loop-2 conformations.
(C) Variable conformation of the protease domain linker (PD linker) revealed by superimposition of the structures from the six protomers based on the β10-β11 hairpin.
(D) Cartoon diagram illustrating the ADP-induced rotational and translational movements of the LonA protomers, made possible by the PD linker (curved lines). Also shown is the interaction between the sensor-I residue (star) and the substrate-binding β10-β11 hairpin (triangle) in the ADP-bound protomer (yellow).
See also the asymmetry in the hexameric structure and the electron density map for the pore loops and loop 2s in Figures S4 and S5.
Structure  , DOI: ( /j.str )
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5. Figure 3
Locations of the Pore Loop and Loop 2 in Nucleotide-Free and ADP-Bound Protomers
(A) Side view of Core-E423Q complex in semi-transparent ribbons, showing the locations of the pore-loop and loop-2 residues, shown as spheres, in the nucleotide-free (blue) and ADP-bound (gold) protomers. The three bound ADPs are shown as magenta sticks. Also indicated are three horizontal layers 1–3 where these loops are distributed. The arrowhead indicates the direction of the central axis (dotted line) of the complex.
(B–D) Top views along the central axis showing the distribution of the pore loops (orange) and loop 2s (green), which are highlighted as semi-transparent spheres colored as in (A), on each section of the layers 1–3 as indicated in (A). The conserved residues are underlined.
(E) Degradation of casein and Ig2 by wild-type (WT) and ΔLoop-2 mutant of MtaLonA by SDS-PAGE and Coomassie blue staining.
Structure  , DOI: ( /j.str )
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6. Figure 4
Structural Coupling of the ATPase Site to the Substrate-Binding Groove
(A and B) ATPase sites in the nucleotide-free protomer A (blue) (A) and ADP-bound protomer B (gold) (B), superimposed based on α13.
(C) The β10-β11 hairpin makes contact with the ATPase site in ADP-bound protomer B, but not in the nucleotide-free protomer A.
(D) Effect of bortezomib on ATPase stimulation in WT-MtaLonA (MtaLonA), MtaLonA mutant Δhairpin, and human LonA (huLonA).
(E and F) Effect of casein (E) and Ig2 (F) on stimulation of the ATPase activity of WT-MtaLonA, and MtaLonA mutants ΔLoop-2 and Δhairpin (n ≥ 3; error bars denote SD).
Structure  , DOI: ( /j.str )
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7. Figure 5
Structural Coupling of the α Domain/PD Linker to the Substrate-Binding Groove
(A) Stereo view of the adjoining protomers A (blue) and B (gray); the former is superimposed with the structure of E. coli LonA protease domain (purple). A copy of the protomer B (gold) is also superimposed with the protomer A.
(B) Degradation of casein and Ig2 by WT and mutants of MtaLonA and huLonA by SDS-PAGE and Coomassie blue staining.
See also the structure of the bound inhibitor and the substrate-binding groove in Figures S6 and S7.
Structure  , DOI: ( /j.str )
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8. Figure 6
Model for the Chemomechanical Operation Illustrating a Non-concerted ATPase Reaction Cycle
Three non-adjacent protomers are cooperatively linked and bind ATP simultaneously, and the two pairs of three cooperatively linked protomers bind and hydrolyze ATP sequentially. Coordinated movements of the functionally important structural elements inside the LonA hexamer are shown in an unwrapped planar diagram on the right. The letters A to F are PDB chain identifiers. Colored arrows depict movements of the functional elements for the subsequent ATPase cycle. A substrate polypeptide (black curve) is shown bound to the protease domain (gray) of protomer C and undergoes processive degradation facilitated by the positive-charged Arg paddle shown as sun crosses. An opened β10-β11 hairpin (blue) induced by the bound substrate (or inhibitor) stimulates allosterically ATPase activity. See also the molecular animations in Movies S1 and S2.
Structure  , DOI: ( /j.str )
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