PDBsum entry 1vqf

DNA binding protein

PDB id: 1vqf

Contents

Protein chain

86 a.a.

Waters ×43

References listed in PDB file

Key reference

Title

Context dependence of mutational effects in a protein: the crystal structures of the V35i, I47V and V35i/i47V gene V protein core mutants.

Authors

H.Zhang, M.M.Skinner, W.S.Sandberg, A.H.Wang, T.C.Terwilliger.

Ref.

J Mol Biol, 1996, 259, 148-159. [DOI no: 10.1006/jmbi.1996.0309]

PubMed id

8648642

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 93%.

Abstract

The basis for the context dependence of the effects of core mutations on protein stability was investigated by comparing the structures of three gene V protein mutants with that of the wild-type protein. We previously examined a "swapped" mutant in which core residues Val35 and Ile47 were simply reversed so that the mutant had no hydrophobicity change from the native protein. The swapped mutant was destabilized by 3 kcal/mol per gene V protein dimer relative to the wild-type protein, demonstrating that factors other than hydrophobicity must make substantial contributions to the effects of mutations on the stability of the protein. Here we have determined the structure of this swapped mutant (V35I/I47V) as well as those of the two constituent mutants (V35I and I47V). We find that the structures of the mutant proteins are very similar to that of the wild-type protein except for the necessary addition or deletion of methylene groups and for slight positional shifts of atoms around each mutated residue. The structure of the double mutant is a composite of the structures of the two single mutants. In the mutant structures, the V35I mutation fills a cavity that exists in the wild-type protein and the I47V mutation creates a new cavity. The structures of the mutants indicate further that the reason the V35I and I47V mutations do not have opposite effects on stability is that the cavity in the wild-type protein filled by the V35I mutation is not optimally shaped for accommodating the additional methylene group of the isoleucine. These results support the concepts that the details of core packing have substantial influence on the effects of core mutations on protein stability and that these packing effects are major determinants of the context dependence of core mutation effects on stability.

Figure 2.
Figure 2. A stereo view of the difference Fourier maps at 1.8 Å showing the difference in electron density between mutants and wild-type gene V protein. Amplitudes (Fmut - FWT ) were used, where Fmut and FWT are the observed structure amplitudes for the mutant and wild-type structure. The phases were calculated from the refined gene V protein model. The V35I and I47V maps are contoured at 3s and the V35I/I47V map at 2.5s for positive and negative contours, where s is the root-mean-square density throughout the cell. Positive and negative electronic densities are displayed in green and red, respectively. Yellow is red and green on top of each other. Coordinates are those for the wild-type gene V protein. Nomenclature for atoms is as follows: CD1 and CD2 are equivalent to C d1 and C d2 , CG1 and CG2 are equivalent to C d1 and C d2 , and CB is equivalent to C b . (a) V35I; (b) I47V; (c) V35I/I47V.

Figure 4.
Figure 4. A close-up stereo view of the superposition of the structures of mutant gene V proteins (I47V, green; V35I, magenta; V35I/I47V, cyan) on the structure of the wild-type protein (yellow lines). The mutant structures were first aligned by least-squares superposition of the main-chain atoms on the wild-type. Only the relevant portions of the structures are shown. The superposition of all mutants closely resemble that of the wild-type model as it is almost impossible to distinguish color differences between the models except at the mutated site. Also, the two single mutants in (a) closely resemble those of the double mutant in (b). For atom nomenclature see the legend to Figure 2. (a) V35I and I47V versus WT; (b) V35I/I47V versus WT.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 148-159) copyright 1996.

Secondary reference #1

Title

Difference refinement: obtaining differences between two related structures.

Authors

T.C.Terwilliger, J.Berendzen.

Ref.

Acta Crystallogr D Biol Crystallogr, 1995, 51, 609-618. [DOI no: 10.1107/S0907444994013247]

PubMed id

15299790

Figure 1.
Fig. 1. The effects of incompleteness of data on model quality for independent refinement (squares) and difference refinement (triangles) of a variant struture for a simulated peptide of 51 atoms. The shift between the known native and variant structures was 0.1 /~; two unmodeiled water molecules were added at the same positions in native and variant structures. (a) The .m.s, errors in the model ariant atomic coordinates. (b) The r.m.s, errors in the displacements from model native to model variant structures.

Figure 3.
Fig. 3. The effects of decreasing the correlation in modeling errors. Conditions were the same as for Fig. 2 except hat the shift between the known native and variant structures was held fixed at 0.1 A r.m.s. while the two unmodelled water molecules were placed at different locations in the know native and variant structures.

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

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

Authors

M.M.Skinner, H.Zhang, D.H.Leschnitzer, Y.Guan, H.Bellamy, R.M.Sweet, C.W.Gray, R.N.Konings, A.H.Wang, T.C.Terwilliger.

Ref.

Proc Natl Acad Sci U S A, 1994, 91, 2071-2075. [DOI no: 10.1073/pnas.91.6.2071]

PubMed id

8134350