Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.

Skinner, Matthew M.; Zhang, Hong; Leschnitzer, D.H.; Guan, Yue; Bellamy, Henry D.; Sweet, Robert M.; Gray, Carla W.; Konings, Ruud N. H.; Wang, Andrew H.‐J.; Terwilliger, Thomas C.

doi:10.1073/pnas.91.6.2071

Cited by 105 publications

(68 citation statements)

References 42 publications

(52 reference statements)

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“…The high-resolution crystal structures of the wt- (Skinner et al, 1994), the Y41F, and Y41H mutant and this work) GVP proteins, and the high-resolution NMR structure of the Y41 mutant afford us a reliable molecular structure of the ssDNA-binding proteins from Ff phages. Our calculation of the electrostatic potential of the GVP in various environments provided insight into the DNA-binding properties.…”

Section: Discussionmentioning

confidence: 69%

“…The structure determination of the wild-type protein by the MAD method has been described before (Skinner et al, 1994).…”

Section: Structure Determination and Refinementmentioning

confidence: 99%

“…The importance of Y41 is that it participates directly in the protein dimer-dimer contacts in the GVP-ssDNA complex (King & Coleman, 1988;Stassen et al, 1992). The three crystal structures revealed that Y41 indeed is involved intimately in the protein-protein contacts, but with two distinct modes Skinner et al, 1994). In the wild-type and Y41F structures, the loop (residues 36-43) that contains the 41 position from one monomer protein interacts with the same loop from the crystallographic twofold symmetry-related monomer protein of a neighboring GVP dimer.…”

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confidence: 99%

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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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Section: Discussionmentioning

confidence: 69%

“…The structure determination of the wild-type protein by the MAD method has been described before (Skinner et al, 1994).…”

Section: Structure Determination and Refinementmentioning

confidence: 99%

mentioning

confidence: 99%

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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 selenomethionine-containing derivative of interleukin-5 was also used to facilitate the solution of its three-dimensional structure by X-ray crystallography . Many other examples have recently been published of selenomethionine-containing derivatives used for solving the crystal structure by multiple anomalous diffraction (Martin et al, 1993 ;Newman et al, 1994;Ramakrishnan et al, 1993;Skinner et al, 1994;Van Duyne et al, 1991 ;Wu et al, 1994).…”

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confidence: 99%

Selenomethionine Labelling of Phosphomannose Isomerase Changes its Kinetic Properties

Bernard¹,

Wells²,

Cleasby³

et al. 1995

European Journal of Biochemistry

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Phosphomannose isomerase (PMI) is an essential enzyme in the early steps of the protein glycosylation pathway in both prokaryotes and eukaryotes. Lack of the enzyme is lethal for fungal organisms and it is thus a potential fungicidal target. To facilitate the solution of the three-dimensional structure of the enzyme from the pathogen Candida albicans, we have produced the recombinant selenomethionine-labelled enzyme (SeMet-PMI). D U l , a methionine auxotroph Escherichia coli strain, was transformed with a PMI expression plasmid and grown on an enriched selenomethionine-containing medium to highcell densities. The SeMet-PMI protein has been purified and found by amino acid analysis to have its methionine residues replaced by selenomethionine residues. Electrospray mass spectroscopy showed a major species of 49063 ? 10 Da for SeMet-PMI compared to 48735 ? 6 Da for the normal recombinant enzyme, accounting for the incorporation of seven selenomethionine residues. SeMet-PMI crystallised isomorphously with the normal PMI protein and the crystals diffract to 0.23 nm. Kinetic characterisation of SeMet-PMI showed that its K, for the substrate mannose-6-phosphate was fourfold higher than that of its methionine-containing counterpart. The inhibition constant for zinc ions was also increased by a similar factor. However, the V,, was unaltered. These results suggested that one or more methionine residues must be in close proximity to the substrate-binding pocket in the active sire, rendering substrate access more difficult compared to the normal enzyme. This hypothesis was confirmed by the finding of four methionine residues lying along one wall of the active site.

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“…Although a definitive view of the complex will be lacking until the three-dimensional structure of a protein-DNA oligonucleotide complex is solved by X-ray crystallography, the crystal structure of the wt-GVP, determined recently (Skinner et al, 1994), as well as two mutants with changes at the tyrosine 41 (Y41) position (Guan et al, 1994), have made it possible to propose a plausible model of the GVP-DNA complex (Skinner et al, 1994;Guan et al, 1995). In particular, the participation of Y41 in the protein dimer-dimer contacts in the GVP-ssDNA complex (King & Coleman, 1988;Stassen et al, 1992) was explained adequately.…”

mentioning

confidence: 99%

Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X‐ray crystallography

Gao

Zhang

et al. 1997

Protein Science

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The high-resolution crystal structure of the gene V protein (GVP) from the Ff filamentous phages (M13, fl, fd) has been solved recently for the wild-type and two surface mutant (Y41F and Y41H) proteins, leading to a plausible model for the polymeric GVP-ssDNA complex (Guan Y, Zhang H, Wang AHJ, 1995, Protein Sci 4187-197). The model of the complex shows extensive contacts between neighboring dimer GVPs involving electrostatic interactions between the K69 from one and the D79 and R82 from the next dimer. In addition, hydrophobic interactions between the amino acids L32 and L44 from one and G23 from the next dimer also contribute to the dimer-dimer interactions. Mutations at the L32, K69, and R82 amino acid sites generally destabilize the protein and many of these affect the function of the phage. We have studied the structural effects of three mutant proteins involving those sites, i.e., L32R, K69H, and R82C, by X-ray crystallographic analysis at 2.0 8, resolution. In L32R GVP, the structural perturbation is localized, whereas in K69H and R82C GVPs, some long-range effects are also detected in addition to the local perturbation. We have interpreted the protein stability and the functional properties associated with those mutations in terms of the observed structural perturbations.

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Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.

Cited by 105 publications

References 42 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

Selenomethionine Labelling of Phosphomannose Isomerase Changes its Kinetic Properties

Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X‐ray crystallography

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