1jk1: Difference between revisions

Revision as of 14:23, 21 February 2008

Zif268 D20A Mutant Bound to WT DNA Site

OverviewOverview

Structural and biochemical studies of Cys(2)His(2) zinc finger proteins initially led several groups to propose a "recognition code" involving a simple set of rules relating key amino acid residues in the zinc finger protein to bases in its DNA site. One recent study from our group, involving geometric analysis of protein-DNA interactions, has discussed limitations of this idea and has shown how the spatial relationship between the polypeptide backbone and the DNA helps to determine what contacts are possible at any given position in a protein-DNA complex. Here we report a study of a zinc finger variant that highlights yet another source of complexity inherent in protein-DNA recognition. In particular, we find that mutations can cause key side-chains to rearrange at the protein-DNA interface without fundamental changes in the spatial relationship between the polypeptide backbone and the DNA. This is clear from a simple analysis of the binding site preferences and co-crystal structures for the Asp20-->Ala point mutant of Zif268. This point mutation in finger one changes the specificity of the protein from GCG TGG GCG to GCG TGG GC(G/T), and we have solved crystal structures of the D20A mutant bound to both types of sites. The structure of the D20A mutant bound to the GCG site reveals that contacts from key residues in the recognition helix are coupled in complex ways. The structure of the complex with the GCT site also shows an important new water molecule at the protein-DNA interface. These side-chain/side-chain interactions, and resultant changes in hydration at the interface, affect binding specificity in ways that cannot be predicted either from a simple recognition code or from analysis of spatial relationships at the protein-DNA interface. Accurate computer modeling of protein-DNA interfaces remains a challenging problem and will require systematic strategies for modeling side-chain rearrangements and change in hydration.

About this StructureAbout this Structure

1JK1 is a Single protein structure of sequence from Mus musculus with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition., Miller JC, Pabo CO, J Mol Biol. 2001 Oct 19;313(2):309-15. PMID:11800559

Page seeded by OCA on Thu Feb 21 13:23:31 2008

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OCA

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-[[Image:1jk1.gif|left|200px]]<br /><applet load="1jk1" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1jk1.gif|left|200px]]<br /><applet load="1jk1" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1jk1, resolution 1.90&Aring;" />
 '''Zif268 D20A Mutant Bound to WT DNA Site'''<br />
 ==Overview==
-Structural and biochemical studies of Cys(2)His(2) zinc finger proteins, initially led several groups to propose a "recognition code" involving a, simple set of rules relating key amino acid residues in the zinc finger, protein to bases in its DNA site. One recent study from our group, involving geometric analysis of protein-DNA interactions, has discussed, limitations of this idea and has shown how the spatial relationship, between the polypeptide backbone and the DNA helps to determine what, contacts are possible at any given position in a protein-DNA complex. Here, we report a study of a zinc finger variant that highlights yet another, source of complexity inherent in protein-DNA recognition. In particular, we find that mutations can cause key side-chains to rearrange at the, protein-DNA interface without fundamental changes in the spatial, relationship between the polypeptide backbone and the DNA. This is clear, from a simple analysis of the binding site preferences and co-crystal, structures for the Asp20--&gt;Ala point mutant of Zif268. This point mutation, in finger one changes the specificity of the protein from GCG TGG GCG to, GCG TGG GC(G/T), and we have solved crystal structures of the D20A mutant, bound to both types of sites. The structure of the D20A mutant bound to, the GCG site reveals that contacts from key residues in the recognition, helix are coupled in complex ways. The structure of the complex with the, GCT site also shows an important new water molecule at the protein-DNA, interface. These side-chain/side-chain interactions, and resultant changes, in hydration at the interface, affect binding specificity in ways that, cannot be predicted either from a simple recognition code or from analysis, of spatial relationships at the protein-DNA interface. Accurate computer, modeling of protein-DNA interfaces remains a challenging problem and will, require systematic strategies for modeling side-chain rearrangements and, change in hydration.
+Structural and biochemical studies of Cys(2)His(2) zinc finger proteins initially led several groups to propose a "recognition code" involving a simple set of rules relating key amino acid residues in the zinc finger protein to bases in its DNA site. One recent study from our group, involving geometric analysis of protein-DNA interactions, has discussed limitations of this idea and has shown how the spatial relationship between the polypeptide backbone and the DNA helps to determine what contacts are possible at any given position in a protein-DNA complex. Here we report a study of a zinc finger variant that highlights yet another source of complexity inherent in protein-DNA recognition. In particular, we find that mutations can cause key side-chains to rearrange at the protein-DNA interface without fundamental changes in the spatial relationship between the polypeptide backbone and the DNA. This is clear from a simple analysis of the binding site preferences and co-crystal structures for the Asp20--&gt;Ala point mutant of Zif268. This point mutation in finger one changes the specificity of the protein from GCG TGG GCG to GCG TGG GC(G/T), and we have solved crystal structures of the D20A mutant bound to both types of sites. The structure of the D20A mutant bound to the GCG site reveals that contacts from key residues in the recognition helix are coupled in complex ways. The structure of the complex with the GCT site also shows an important new water molecule at the protein-DNA interface. These side-chain/side-chain interactions, and resultant changes in hydration at the interface, affect binding specificity in ways that cannot be predicted either from a simple recognition code or from analysis of spatial relationships at the protein-DNA interface. Accurate computer modeling of protein-DNA interfaces remains a challenging problem and will require systematic strategies for modeling side-chain rearrangements and change in hydration.
 ==About this Structure==
-JK1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JK1 OCA].
+JK1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JK1 OCA].
 ==Reference==
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 [[Category: Mus musculus]]
 [[Category: Single protein]]
-[[Category: Miller, J.C.]]
+[[Category: Miller, J C.]]
-[[Category: Pabo, C.O.]]
+[[Category: Pabo, C O.]]
 [[Category: ZN]]
 [[Category: double-stranded dna]]
@@ Line 20: / Line 20: @@
 [[Category: zinc finger]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:20:13 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:23:31 2008''