Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target.
Phage T4 protects its DNA from the two-gene-encoded gmrS/gmrD (glucose-modified hydroxymethylcytosine restriction endonuclease) CT of pathogenic Escherichia coli, CT596, by injecting several hundred copies of the 76-amino-acid-residue nuclease inhibitor, IPI*, into the infected host. Here, the three-dimensional solution structure of mature IPI* is reported as determined by nuclear magnetic resonance techniques using 1290 experimental nuclear Overhauser effect and dipolar coupling constraints ( approximately 17 constraints per residue). Close examination of this oblate-shaped protein structure reveals a novel fold consisting of two small beta-sheets (beta1: B1 and B2; beta2: B3-B5) flanked at the N- and C-termini by alpha-helices (H1 and H2). Such a fold is very compact in shape and allows ejection of IPI* through the narrow 30-A portal and tail tube apertures of the virion without unfolding. Structural and dynamic measurements identify an exposed hydrophobic knob that is a putative gmrS/gmrD-binding site. A single gene from the uropathogenic E. coli UT189, which codes for a gmrS/gmrD-like UT fusion enzyme (with approximately 90% identity to the heterodimeric CT enzyme), has evolved IPI* inhibitor immunity. Analysis of the gmrS/gmrD restriction endonuclease enzyme family and its IPI* family phage antagonists reveals an evolutionary pathway that has elaborated a surprisingly diverse and specifically fitted set of coevolving attack and defense structures.
Rifat
Dalin
D
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201-1503, USA.
Wright
Nathan T
NT
Varney
Kristen M
KM
Weber
David J
DJ
Black
Lindsay W
LW
D000595:Amino Acid Sequence; D017122:Bacteriophage T4 / Q000201:enzymology*; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism; D004262:DNA Restriction Enzymes / Q000737:chemistry* / Q000235:genetics; D004279:DNA, Viral / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology* / Q000472:pathogenicity / Q000821:virology; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D015698:Genomic Library; D006031:Glycosylation; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D016366:Open Reading Frames; D010957:Plasmids; D011110:Polymorphism, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013379:Substrate Specificity; D013696:Temperature
D036022:Capsid Proteins; D004279:DNA, Viral; D029968:Escherichia coli Proteins; D011994:Recombinant Proteins; C046947:internal protein I, bacteriophage T4; D003596:Cytosine; D004262:DNA Restriction Enzymes