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2aje

From Proteopedia

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[[Image:2aje.gif|left|200px]]
 
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{{Structure
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==Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain==
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|PDB= 2aje |SIZE=350|CAPTION= <scene name='initialview01'>2aje</scene>
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<StructureSection load='2aje' size='340' side='right'caption='[[2aje]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<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>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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|GENE=
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<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>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[1w0t|1W0T]], [[1w0u|1W0U]], [[1ign|1IGN]], [[1fex|1FEX]], [[1ba5|1BA5]], [[1msf|1MSF]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aje OCA], [http://www.ebi.ac.uk/pdbsum/2aje PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2aje RCSB]</span>
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[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.
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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'''Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain'''
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aj/2aje_consurf.spt"</scriptWhenChecked>
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==Overview==
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== 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.
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==About this Structure==
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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>
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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].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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]
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</div>
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<div class="pdbe-citations 2aje" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cheng, Y H.]]
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[[Category: Cheng YH]]
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[[Category: Chung, B C.]]
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[[Category: Chung BC]]
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[[Category: Hsiao, H H.]]
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[[Category: Hsiao HH]]
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[[Category: Huang, T H.]]
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[[Category: Huang TH]]
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[[Category: Sue, S C.]]
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[[Category: Sue SC]]
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[[Category: dna-binding]]
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[[Category: myb motif]]
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[[Category: telomere]]
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[[Category: trp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:53:28 2008''
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Current revision

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

PDB ID 2aje

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