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PDBsum entry 2apu

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Hydrolase PDB id
2apu
Jmol
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Protein chains
(+ 50 more) 136 a.a.

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Title Amyloid-Like fibrils of ribonuclease a with three-Dimensional domain-Swapped and native-Like structure.
Authors S.Sambashivan, Y.Liu, M.R.Sawaya, M.Gingery, D.Eisenberg.
Ref. Nature, 2005, 437, 266-269. [DOI no: 10.1038/nature03916]
PubMed id 16148936
Abstract
Amyloid or amyloid-like fibrils are elongated, insoluble protein aggregates, formed in vivo in association with neurodegenerative diseases or in vitro from soluble native proteins, respectively. The underlying structure of the fibrillar or 'cross-beta' state has presented long-standing, fundamental puzzles of protein structure. These include whether fibril-forming proteins have two structurally distinct stable states, native and fibrillar, and whether all or only part of the native protein refolds as it converts to the fibrillar state. Here we show that a designed amyloid-like fibril of the well-characterized enzyme RNase A contains native-like molecules capable of enzymatic activity. In addition, these functional molecular units are formed from a core RNase A domain and a swapped complementary domain. These findings are consistent with the zipper-spine model in which a cross-beta spine is decorated with three-dimensional domain-swapped functional units, retaining native-like structure.
Figure 1.
Figure 1: RNase A monomer and C-terminal domain-swapped dimer and the 3D domain-swapped zipper-spine model. a, The RNase A monomer is stabilized by four disulphide bonds Cys 26 -Cys 84, Cys 40 -Cys 95, Cys 58 -Cys 110 and Cys 65 -Cys 72, hindering conformational changes. His 12 in the core of the protein and His 119 on the -strand that is swapped (shown by sticks) are active-site residues that we mutate to test for activity by complementation. b, The C-terminal domain-swapped dimer is formed by exchanging the C-terminal -strands between two monomers. The hinge loop (residues 112 -115) has been expanded by inserting the sequence -GQ[10]G-. c, Diagram of amyloid-like fibril formation in RNase A with Q[10] expansion, leading to a runaway domain swap. The Q[10]-H12A mutants are shown in blue and the Q[10]-H119A mutants in green. Domain swapping between two mutants complements active sites.
Figure 2.
Figure 2: Properties of the RNase A amyloid-like fibrils. The hinge-loop region of wild-type RNase A that connects the C-terminal -strand (triangle in the diagrams in column 1) to the protein core is expanded with the -GQ[10]G- motif to generate amyloid-forming RNase A mutants. Two inactive RNase A mutants are formed by replacing His 12 or His 119 with Ala. Wild-type RNase A does not form fibrils and has a fully functional active site (row 1, columns 2 and 4). The Q[10]-H12A, Q[10]-H119A and Q[10]-H12A + Q[10]-H119A constructs all form amyloid-like fibrils (column 2) and bind Congo red with the characteristic apple-green birefringence (column 3). The Q[10]-H12A + Q[10]-H119A fibrils (row 4, column 4) have significantly higher activity than fibrils of Q[10]-H12A (row 2, column 4) and Q[10]-H119A (row 3, column 4) alone. This is a result of complementation of active sites by domain swapping. The expected activity of each of the constructs is given in parentheses. Scale bar (column 2), 200 nm.
The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 437, 266-269) copyright 2005.
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