1kqq: Difference between revisions

Revision as of 14:37, 21 February 2008

Solution Structure of the Dead ringer ARID-DNA Complex

OverviewOverview

The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.

About this StructureAbout this Structure

1KQQ is a Single protein structure of sequence from Drosophila melanogaster. Full crystallographic information is available from OCA.

ReferenceReference

The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA., Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT, EMBO J. 2002 Mar 1;21(5):1197-209. PMID:11867548

Page seeded by OCA on Thu Feb 21 13:37:01 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1kqq.gif|left|200px]]<br /><applet load="1kqq" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kqq.gif|left|200px]]<br /><applet load="1kqq" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1kqq" />
 '''Solution Structure of the Dead ringer ARID-DNA Complex'''<br />
 ==Overview==
-The AT-rich interaction domain (ARID) is a DNA-binding module found in, many eukaryotic transcription factors. Using NMR spectroscopy, we have, determined the first ever three-dimensional structure of an ARID--DNA, complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila, melanogaster. ARIDs recognize DNA through a novel mechanism involving, major groove immobilization of a large loop that connects the helices of a, non-canonical helix-turn-helix motif, and through a concomitant structural, rearrangement that produces stabilizing contacts from a beta-hairpin. Dead, ringer's preference for AT-rich DNA originates from three positions within, the ARID fold that form energetically significant contacts to an, adenine-thymine base step. Amino acids that dictate binding specificity, are not highly conserved, suggesting that ARIDs will bind to a range of, nucleotide sequences. Extended ARIDs, found in several sequence-specific, transcription factors, are distinguished by the presence of a C-terminal, helix that may increase their intrinsic affinity for DNA. The prevalence, of serine amino acids at all specificity determining positions suggests, that ARIDs within SWI/SNF-related complexes will interact with DNA, non-sequence specifically.
+The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.
 ==About this Structure==
-KQQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KQQ OCA].
+KQQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQQ OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Drosophila melanogaster]]
 [[Category: Single protein]]
-[[Category: Clubb, R.T.]]
+[[Category: Clubb, R T.]]
-[[Category: Daughdrill, G.W.]]
+[[Category: Daughdrill, G W.]]
 [[Category: Ford, J.]]
 [[Category: Iwahara, J.]]
@@ Line 21: / Line 21: @@
 [[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:40:57 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:37:01 2008''