Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-01-22

AUTHORS

Jenny Keller, Nicolas Leulliot, Christian Cambillau, Valérie Campanacci, Stéphanie Porciero, David Prangishvili, Patrick Forterre, Diego Cortez, Sophie Quevillon-Cheruel, Herman van Tilbeurgh

ABSTRACT

The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 A resolution. The structure of AFV3-109 is a five stranded beta-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes. More... »

PAGES

12-12

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1743-422x-4-12

DOI

http://dx.doi.org/10.1186/1743-422x-4-12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1044572045

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17241456


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24 schema:description The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 A resolution. The structure of AFV3-109 is a five stranded beta-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
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31 schema:keywords AFV3
32 AFV3 ORF 109
33 Acidianus Filamentous Virus 3
34 Bicaudaviridae
35 Data Bank
36 Filamentous Virus 3
37 Firmicutes
38 Lipothrixviridae
39 ORF 109
40 ORF109
41 Protein Data Bank
42 Rudiviridae
43 STIV
44 STIV1
45 STIV1 protein
46 Sulfolobus
47 acid
48 analysis
49 archaea
50 bacterial homolog
51 banks
52 cavity
53 charge distribution
54 code
55 conserved gene
56 cradle
57 crenarchaeal viruses
58 crystal forms
59 crystal structure
60 database
61 different crystal forms
62 dimer
63 distribution
64 dsDNA
65 eukaryotic viruses
66 extend
67 extent databases
68 extraordinary morphology
69 familes
70 fluorescence
71 fluorescence titration
72 folds
73 form
74 function
75 function of AFV3
76 genes
77 genome
78 genome codes
79 genomes of members
80 genomic sequence analysis
81 glycerol
82 helix
83 homolog
84 homology
85 hyperthermophilic archaea
86 icosahedral viruses
87 interaction
88 large extend
89 loop
90 members
91 morphology
92 nucleic acids
93 orthologs
94 part
95 pool
96 prophage sequences
97 protein
98 region
99 related folds
100 related sequences
101 residues
102 resolution
103 sequence
104 sequence analysis
105 shape
106 side
107 size
108 small pool
109 solution
110 structural homology
111 structure
112 structure of AFV3
113 subset
114 titration
115 unclassified Sulfolobus
116 unidentified prophage sequences
117 viral familes
118 virus
119 virus 3
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