2aje

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:18, 15 May 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2aje.gif|left|200px]]
 
-
<!--
+
==Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain==
-
The line below this paragraph, containing "STRUCTURE_2aje", creates the "Structure Box" on the page.
+
<StructureSection load='2aje' size='340' side='right'caption='[[2aje]]' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2aje]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AJE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AJE FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
-->
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aje OCA], [https://pdbe.org/2aje PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aje RCSB], [https://www.ebi.ac.uk/pdbsum/2aje PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aje ProSAT]</span></td></tr>
-
{{STRUCTURE_2aje| PDB=2aje | SCENE= }}
+
</table>
-
 
+
== Function ==
-
'''Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain'''
+
[https://www.uniprot.org/uniprot/TRP1_ARATH TRP1_ARATH] Binds specifically to the plant telomeric double-stranded DNA sequences 5'-GGTTTAG-3'. At least 4 repeats of telomeric sequences are required for binding. Induces DNA bending.
-
 
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
==Overview==
+
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aj/2aje_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2aje ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1(464-560)), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1(464-560) binds to a 13-mer DNA duplex containing a single repeat of an A.thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a K(D) approximately 10(-6)-10(-7) M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1(464-560) is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1(464-560) induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.
The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1(464-560)), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1(464-560) binds to a 13-mer DNA duplex containing a single repeat of an A.thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a K(D) approximately 10(-6)-10(-7) M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1(464-560) is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1(464-560) induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.
-
==About this Structure==
+
Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: a new fold with an additional C-terminal helix.,Sue SC, Hsiao HH, Chung BC, Cheng YH, Hsueh KL, Chen CM, Ho CH, Huang TH J Mol Biol. 2006 Feb 10;356(1):72-85. Epub 2005 Nov 22. PMID:16337232<ref>PMID:16337232</ref>
-
2AJE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AJE OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: a new fold with an additional C-terminal helix., Sue SC, Hsiao HH, Chung BC, Cheng YH, Hsueh KL, Chen CM, Ho CH, Huang TH, J Mol Biol. 2006 Feb 10;356(1):72-85. Epub 2005 Nov 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16337232 16337232]
+
</div>
 +
<div class="pdbe-citations 2aje" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Cheng, Y H.]]
+
[[Category: Cheng YH]]
-
[[Category: Chung, B C.]]
+
[[Category: Chung BC]]
-
[[Category: Hsiao, H H.]]
+
[[Category: Hsiao HH]]
-
[[Category: Huang, T H.]]
+
[[Category: Huang TH]]
-
[[Category: Sue, S C.]]
+
[[Category: Sue SC]]
-
[[Category: Dna-binding]]
+
-
[[Category: Myb motif]]
+
-
[[Category: Telomere]]
+
-
[[Category: Trp]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:07:27 2008''
+

Current revision

Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain

PDB ID 2aje

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2aje"
Personal tools