The amino acid sequence of gene 5 protein of bacteriophage M 13

Cuypers, Theo; Ouderaa, Frans J. van der; Jong, Wilfried W. de

doi:10.1016/s0006-291x(74)80016-1

Cited by 63 publications

(21 citation statements)

References 22 publications

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“…As the first step toward this goal, we have recently determined the crystal structure of the wt-GVP (Skinner 187 (Cuypers et at., 1974) with those amino acids that are in contact with DNA marked in boxes. R: Topology diagram of the secondary structure of the gene V protein dimer.…”

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Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: A model of the GVP‐ssDNA complex

1995

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The crystal structure of the gene V protein (GVP) from the Ff filamentous phages (M13, f l , fd) has been solved for the wild-type and two mutant (Y41F and Y41H) proteins at high resolution. The Y41H mutant crystal structure revealed crystal packing interactions, which suggested a plausible scheme for constructing the polymeric protein shell of the GVP-single-stranded DNA (ssDNA) complex (Guan Y, et al., 1994, Biochemistry 33:7768-7778). The electrostatic potentials of the isolated and the cooperatively formed protein shell have been calculated using the program GRASP and they revealed a highly asymmetric pattern of the electrostatic charge distribution. The inner surface of the putative DNA-binding channel is positively charged, whereas the opposite outer surface is nearly neutral. The electrostatic calculation further demonstrated that the formation of the helical protein shell enhanced the asymmetry of the electrostatic distribution. A model of the GVP-ssDNA complex with the n = 4 DNA-binding mode could be built with only minor conformational perturbation to the GVP protein shell. The model is consistent with existing biochemical and biophysical data and provides clues to the properties of GVP, including the high cooperativity of the protein binding to ssDNA. The two antiparallel ssDNA strands form a helical ribbon with the sugar-phosphate backbones at the middle and the bases pointing away from each other. The bases are stacked and the Phe 73 residue is intercalated between two bases. The optimum binding to a tetranucleotide unit requires the participation of four GVP dimers, which may explain the cooperativity of the GVP binding to DNA.

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Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: A model of the GVP‐ssDNA complex

1995

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“…Thus far, the positively charged R16 and R21, the aliphatic L28, and the aromatic Y26 and F73 residues appear to be firmly established as the amino acids involved (Stassen et al, 1992a,b;King & Coleman, 1988). Furthermore, it has been suggested that Y41 is involved in the protein dimer4imer contacts in 0 1994 American Chemical Society I M I K V E I K P S Q A Q F T T R S G V S z o z i R Q G K P Y S L N E Q L C Y V D L G N E i o 4 1 Y P V L V K I T L D E G Q P A Y A P G L 6 o 6 i Y T V H L S S F K V G Q F G S L M I D R s o FIGURE 1: Amino acid sequence of GVP (Cuypers et al, 1974).…”

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Crystal Structures of Y41H and Y41F Mutants of Gene V Protein from Ff Phage Suggest Possible Protein-Protein Interactions in the GVP-ssDNA Complex

Guan¹,

Zhang²,

Konings³

et al. 1994

Biochemistry

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Gene V protein (GVP) encoded by the filamentous phage Ff (M13, fl, fd) is a homodimeric protein of 87 amino acids that binds to single-stranded DNA (ssDNA) nonspecifically and cooperatively. The structure (monoclinic C2 form) of the wild-type protein has been determined and refined at 1.8-A resolution [Skinner et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2071-2075]. The monomer structure consists of a somewhat distorted five-stranded beta-barrel core with three prominent loops: a DNA-binding loop, a dyad loop, and a dimer contact loop. The amino acid residue at position 41 plays an important role in the dimer-dimer interactions of the protein-ssDNA complex. Two Y41 mutant structures have been studied by X-ray crystallography. The Y41F GVP structure has been refined to an R-factor of 0.180 at 2.2-A resolution and is very similar to the wild-type (wt) structure (rmsd of all C alpha atoms = 0.30 A). In contrast, Y41H GVP forms a new crystal lattice in the space group P2(1)2(1)2(1) with a = 77.18 A, b = 84.17 A, and c = 28.62 A. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-A resolution. The two monomers of Y41H are crystallographically independent, and their structures remain similar to wt-GVP but with significant differences, particularly in the DNA-binding hairpin region. In both crystals, the loop (residues 36-43) that contains the Y41 residue is involved in the crystal dimer packings but in a different manner. The dimer-dimer contacts found in the wt-GVP crystal may be important for GVP aggregation in the absence of DNA. In the presence of DNA, the dimer-dimer contacts may switch to the type found in the Y41H crystal, allowing the GVP-ssDNA complex to form cooperatively. A model of the complex, consistent with existing biochemical and biophysical data, has been constructed from those crystal packing data.

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“…The three most commonly studied members of the group of filamentous coliphages, bacteriophages fl, fd, and M13, are closely related (6,29) and are presumably derived from a common ancestor. Although the amino acid sequence of the major coat protein has been shown to be the same for all three viruses (1,5,21), these viruses can be distinguished on serological grounds (31), and early studies revealed significant differences in the distribution of sequences of consecutive pyrimidine nucleotides in their DNA molecules (13,43), in the products of cleavage of the RFI DNA by restriction endonucleases (45), and in their susceptibility to bacterial restriction (29). The complete sequences of nucleotides in the DNAs of bacteriophages fd (2) and M13 (46) and the structures of several fragments of phage fl DNA (9,25,27,28,35) have been published.…”

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Nucleotide sequence of bacteriophage f1 DNA

Hill¹,

Petersen²

1982

J Virol

131

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The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.

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The amino acid sequence of gene 5 protein of bacteriophage M 13

Cited by 63 publications

References 22 publications

Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: A model of the GVP‐ssDNA complex

Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: A model of the GVP‐ssDNA complex

Crystal Structures of Y41H and Y41F Mutants of Gene V Protein from Ff Phage Suggest Possible Protein-Protein Interactions in the GVP-ssDNA Complex

Nucleotide sequence of bacteriophage f1 DNA

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