1j5n: Difference between revisions

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[[Image:1j5n.gif|left|200px]]<br /><applet load="1j5n" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1j5n.gif|left|200px]]<br /><applet load="1j5n" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1j5n" />

'''Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA'''<br />

==Overview==

NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces, cerevisiae which belongs to the HMGB protein family. Previously, we have, solved the structure of NHP6A in the absence of DNA and modeled its, interaction with DNA. Here, we present the refined solution structures of, the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and, bound forms of the protein adopt the typical L-shaped HMGB domain fold., The DNA in the complex undergoes significant structural rearrangement from, its free form while the protein shows smaller but significant, conformational changes in the complex. Structural and mutational analysis, as well as comparison of the complex with the free DNA provides insight, into the factors that contribute to binding site selection and DNA, deformations in the complex. Further insight into the amino acid, determinants of DNA binding by HMGB domain proteins is given by a, correlation study of NHP6A and 32 other HMGB domains belonging to both the, DNA-sequence-specific and non-sequence-specific families of HMGB proteins., The resulting correlations can be rationalized by comparison of solved, structures of HMGB proteins.

NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces cerevisiae which belongs to the HMGB protein family. Previously, we have solved the structure of NHP6A in the absence of DNA and modeled its interaction with DNA. Here, we present the refined solution structures of the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and bound forms of the protein adopt the typical L-shaped HMGB domain fold. The DNA in the complex undergoes significant structural rearrangement from its free form while the protein shows smaller but significant conformational changes in the complex. Structural and mutational analysis as well as comparison of the complex with the free DNA provides insight into the factors that contribute to binding site selection and DNA deformations in the complex. Further insight into the amino acid determinants of DNA binding by HMGB domain proteins is given by a correlation study of NHP6A and 32 other HMGB domains belonging to both the DNA-sequence-specific and non-sequence-specific families of HMGB proteins. The resulting correlations can be rationalized by comparison of solved structures of HMGB proteins.

==About this Structure==

1J5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1J5N OCA].

1J5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5N OCA].

==Reference==

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[[Category: Saccharomyces cerevisiae]]

[[Category: Single protein]]

[[Category: Allain, F.H.T.]]

[[Category: Allain, F H.T.]]

[[Category: Feigon, J.]]

[[Category: Johnson, R.C.]]

[[Category: Johnson, R C.]]

[[Category: Masse, J.E.]]

[[Category: Masse, J E.]]

[[Category: Wong, B.]]

[[Category: Yen, Y.M.]]

[[Category: Yen, Y M.]]

[[Category: alpha helix]]

[[Category: double helix]]

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[[Category: protein-dna complex]]

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@@ Line 1: / Line 1: @@
-[[Image:1j5n.gif|left|200px]]<br /><applet load="1j5n" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1j5n.gif|left|200px]]<br /><applet load="1j5n" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1j5n" />
 '''Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA'''<br />
 ==Overview==
-NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces, cerevisiae which belongs to the HMGB protein family. Previously, we have, solved the structure of NHP6A in the absence of DNA and modeled its, interaction with DNA. Here, we present the refined solution structures of, the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and, bound forms of the protein adopt the typical L-shaped HMGB domain fold., The DNA in the complex undergoes significant structural rearrangement from, its free form while the protein shows smaller but significant, conformational changes in the complex. Structural and mutational analysis, as well as comparison of the complex with the free DNA provides insight, into the factors that contribute to binding site selection and DNA, deformations in the complex. Further insight into the amino acid, determinants of DNA binding by HMGB domain proteins is given by a, correlation study of NHP6A and 32 other HMGB domains belonging to both the, DNA-sequence-specific and non-sequence-specific families of HMGB proteins., The resulting correlations can be rationalized by comparison of solved, structures of HMGB proteins.
+NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces cerevisiae which belongs to the HMGB protein family. Previously, we have solved the structure of NHP6A in the absence of DNA and modeled its interaction with DNA. Here, we present the refined solution structures of the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and bound forms of the protein adopt the typical L-shaped HMGB domain fold. The DNA in the complex undergoes significant structural rearrangement from its free form while the protein shows smaller but significant conformational changes in the complex. Structural and mutational analysis as well as comparison of the complex with the free DNA provides insight into the factors that contribute to binding site selection and DNA deformations in the complex. Further insight into the amino acid determinants of DNA binding by HMGB domain proteins is given by a correlation study of NHP6A and 32 other HMGB domains belonging to both the DNA-sequence-specific and non-sequence-specific families of HMGB proteins. The resulting correlations can be rationalized by comparison of solved structures of HMGB proteins.
 ==About this Structure==
-J5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J5N OCA].
+J5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5N OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Saccharomyces cerevisiae]]
 [[Category: Single protein]]
-[[Category: Allain, F.H.T.]]
+[[Category: Allain, F H.T.]]
 [[Category: Feigon, J.]]
-[[Category: Johnson, R.C.]]
+[[Category: Johnson, R C.]]
-[[Category: Masse, J.E.]]
+[[Category: Masse, J E.]]
 [[Category: Wong, B.]]
-[[Category: Yen, Y.M.]]
+[[Category: Yen, Y M.]]
 [[Category: alpha helix]]
 [[Category: double helix]]
@@ Line 25: / Line 25: @@
 [[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:57:46 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:19:11 2008''