3IKK

Crystal structure analysis of msp domain

Summary for 3IKK

• Entry DOI: 10.2210/pdb3ikk/pdb
• Descriptor: Vesicle-associated membrane protein-associated protein B/C (2 entities in total)
• Functional Keywords: vapb msp, alternative splicing, amyotrophic lateral sclerosis, cell membrane, coiled coil, disease mutation, host-virus interaction, membrane, neurodegeneration, phosphoprotein, transmembrane, membrane protein
• Biological source: Homo sapiens (human)
• Cellular location: Endoplasmic reticulum membrane; Single-pass type IV membrane protein (By similarity): O95292
• Total number of polymer chains: 2
• Total formula weight: 28720.98

Authors

Shi, J.,Lua, S.,Song, J. (deposition date: 2009-08-06, release date: 2010-05-26, Last modification date: 2024-10-16)

Primary citation

Shi, J.,Lua, S.,Tong, J.S.,Song, J.
Elimination of the native structure and solubility of the hVAPB MSP domain by the Pro56Ser mutation that causes amyotrophic lateral sclerosis.
Biochemistry, 49:3887-3897, 2010

PubMed Abstract: The Pro56Ser mutation in the human VAPB MSP domain causes a familial amyotrophic lateral sclerosis. Here we present the first structural investigation of both wild-type and Pro56Ser mutant MSP domains. The results reveal that the wild-type MSP domain is well-folded at neutral pH but can undergo acid-induced unfolding reversibly. It has a thermodynamic stability energy (DeltaG degrees (N-U)) of 7.40 kcal/mol and is also active in binding to a Nir2 peptide with a K(D) of 0.65 muM. Further determination of its crystal structure reveals that it adopts a seven-strand immunoglobulin-like beta sandwich in which Pro56 adopts the unusual cis-peptide bond conformation that appears to be critical in maintaining the characteristic S-shaped loop. Markedly, the Pro56Ser mutation renders the MSP domain insoluble in buffer. Nevertheless, as facilitated by our recent discovery that "insoluble proteins" can be solubilized in salt-free water, we have successfully characterized the residue-specific conformation of the Pro56Ser mutant by CD and heteronuclear NMR spectroscopy. The Pro56Ser mutant remains lacking of the native tight packing and secondary structures under various conditions and was further characterized as having a non-native helical conformation weakly populated at pH 3.5. Intriguingly, Pro12 located in another S-shaped loop also adopts the cis-peptide bond conformation, and its mutation to Ser is able to make the MSP domain highly insoluble and unfolded like the Pro56Ser mutant. Our study thus implies that the Pro56Ser mutation might lead to ALS by eliminating the native MSP structure, which consequently leads to aggregation and loss of functions under physiological conditions.

PubMed: 20377183
DOI: 10.1021/bi902057a

Experimental method

X-RAY DIFFRACTION (2.5 Å)