Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex

Yue Guan, Hong Zhang, Ruud N H Konings, Cornelis W. Hilbers, Thomas C. Terwilliger, Andrew H J Wang

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Abstract

Gene V protein (GVP) encoded by the filamentous phage Ff (M13, f1, 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-Å 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 β-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-Å resolution and is very similar to the wild-type (wt) structure (rmsd of all Cα atoms = 0.30 Å). In contrast, Y41H GVP forms a new crystal lattice in the space group P212121 with a = 77.18 Å, b = 84.17 Å, and c = 28.62 Å. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-Å 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.

Original languageEnglish (US)
Pages (from-to)7768-7778
Number of pages11
JournalBiochemistry
Volume33
Issue number25
StatePublished - 1994

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Bacteriophage M13
Bacteriophages
Single-Stranded DNA
Genes
Crystal structure
Dimers
Proteins
R388
Crystals
DNA
Monomers
Amino Acids
X ray crystallography
X Ray Crystallography
Crystal lattices
Agglomeration
Switches

ASJC Scopus subject areas

  • Biochemistry

Cite this

Guan, Y., Zhang, H., Konings, R. N. H., Hilbers, C. W., Terwilliger, T. C., & Wang, A. H. J. (1994). Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex. Biochemistry, 33(25), 7768-7778.

Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex. / Guan, Yue; Zhang, Hong; Konings, Ruud N H; Hilbers, Cornelis W.; Terwilliger, Thomas C.; Wang, Andrew H J.

In: Biochemistry, Vol. 33, No. 25, 1994, p. 7768-7778.

Research output: Contribution to journalArticle

Guan, Y, Zhang, H, Konings, RNH, Hilbers, CW, Terwilliger, TC & Wang, AHJ 1994, 'Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex', Biochemistry, vol. 33, no. 25, pp. 7768-7778.
Guan, Yue ; Zhang, Hong ; Konings, Ruud N H ; Hilbers, Cornelis W. ; Terwilliger, Thomas C. ; Wang, Andrew H J. / Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex. In: Biochemistry. 1994 ; Vol. 33, No. 25. pp. 7768-7778.
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title = "Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex",
abstract = "Gene V protein (GVP) encoded by the filamentous phage Ff (M13, f1, 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-{\AA} 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 β-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-{\AA} resolution and is very similar to the wild-type (wt) structure (rmsd of all Cα atoms = 0.30 {\AA}). In contrast, Y41H GVP forms a new crystal lattice in the space group P212121 with a = 77.18 {\AA}, b = 84.17 {\AA}, and c = 28.62 {\AA}. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-{\AA} 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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T1 - Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex

AU - Guan, Yue

AU - Zhang, Hong

AU - Konings, Ruud N H

AU - Hilbers, Cornelis W.

AU - Terwilliger, Thomas C.

AU - Wang, Andrew H J

PY - 1994

Y1 - 1994

N2 - Gene V protein (GVP) encoded by the filamentous phage Ff (M13, f1, 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-Å 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 β-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-Å resolution and is very similar to the wild-type (wt) structure (rmsd of all Cα atoms = 0.30 Å). In contrast, Y41H GVP forms a new crystal lattice in the space group P212121 with a = 77.18 Å, b = 84.17 Å, and c = 28.62 Å. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-Å 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.

AB - Gene V protein (GVP) encoded by the filamentous phage Ff (M13, f1, 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-Å 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 β-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-Å resolution and is very similar to the wild-type (wt) structure (rmsd of all Cα atoms = 0.30 Å). In contrast, Y41H GVP forms a new crystal lattice in the space group P212121 with a = 77.18 Å, b = 84.17 Å, and c = 28.62 Å. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-Å 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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