5EZU

Crystal structure of the N-terminal domain of vaccinia virus immunomodulator A46 in complex with myristic acid.

Summary for 5EZU

• Entry DOI: 10.2210/pdb5ezu/pdb
• Descriptor: Protein A46, MYRISTIC ACID (3 entities in total)
• Functional Keywords: immunomodulator, beta sheet, ab initio phasing, vaccinia virus, a46, viral protein, fatty acids, myristic acid
• Biological source: Vaccinia virus (strain Western Reserve) (VACV)
• Total number of polymer chains: 2
• Total formula weight: 20302.71

Authors

Fedosyuk, S.,Bezerra, G.A.,Sammito, M.,Uson, I.,Skern, T. (deposition date: 2015-11-26, release date: 2016-11-30, Last modification date: 2024-05-08)

Primary citation

Fedosyuk, S.,Bezerra, G.A.,Radakovics, K.,Smith, T.K.,Sammito, M.,Bobik, N.,Round, A.,Ten Eyck, L.F.,Djinovic-Carugo, K.,Uson, I.,Skern, T.
Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins.
PLoS Pathog., 12:e1006079-e1006079, 2016

PubMed Abstract: Vaccinia virus interferes with early events of the activation pathway of the transcriptional factor NF-kB by binding to numerous host TIR-domain containing adaptor proteins. We have previously determined the X-ray structure of the A46 C-terminal domain; however, the structure and function of the A46 N-terminal domain and its relationship to the C-terminal domain have remained unclear. Here, we biophysically characterize residues 1-83 of the N-terminal domain of A46 and present the X-ray structure at 1.55 Å. Crystallographic phases were obtained by a recently developed ab initio method entitled ARCIMBOLDO_BORGES that employs tertiary structure libraries extracted from the Protein Data Bank; data analysis revealed an all β-sheet structure. This is the first such structure solved by this method which should be applicable to any protein composed entirely of β-sheets. The A46(1-83) structure itself is a β-sandwich containing a co-purified molecule of myristic acid inside a hydrophobic pocket and represents a previously unknown lipid-binding fold. Mass spectrometry analysis confirmed the presence of long-chain fatty acids in both N-terminal and full-length A46; mutation of the hydrophobic pocket reduced the lipid content. Using a combination of high resolution X-ray structures of the N- and C-terminal domains and SAXS analysis of full-length protein A46(1-240), we present here a structural model of A46 in a tetrameric assembly. Integrating affinity measurements and structural data, we propose how A46 simultaneously interferes with several TIR-domain containing proteins to inhibit NF-κB activation and postulate that A46 employs a bipartite binding arrangement to sequester the host immune adaptors TRAM and MyD88.

PubMed: 27973613
DOI: 10.1371/journal.ppat.1006079

Experimental method

X-RAY DIFFRACTION (1.55 Å)