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.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201-1503, USA.
Dalin
D
Rifat
Nathan T
NT
Wright
Kristen M
KM
Varney
David J
DJ
Weber
Lindsay W
LW
Black
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