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| | ==VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE== | | ==VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE== |
| - | <StructureSection load='1nk3' size='340' side='right'caption='[[1nk3]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1nk3' size='340' side='right'caption='[[1nk3]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1nk3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NK3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NK3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1nk3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NK3 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nk2|1nk2]]</div></td></tr> | + | </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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=1nk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk3 OCA], [https://pdbe.org/1nk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nk3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nk3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk3 OCA], [http://pdbe.org/1nk3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nk3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nk3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nk3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VND_DROME VND_DROME]] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm. | + | [https://www.uniprot.org/uniprot/VND_DROME VND_DROME] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Drome]] | + | [[Category: Drosophila melanogaster]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ferretti, J A]] | + | [[Category: Ferretti JA]] |
| - | [[Category: Gruschus, J M]] | + | [[Category: Gruschus JM]] |
| - | [[Category: Nirenberg, M]] | + | [[Category: Nirenberg M]] |
| - | [[Category: Tsao, D H.H]] | + | [[Category: Tsao DHH]] |
| - | [[Category: Wang, L H]] | + | [[Category: Wang L-H]] |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Dna-binding protein]]
| + | |
| - | [[Category: Embryonic development]]
| + | |
| - | [[Category: Homeobox]]
| + | |
| - | [[Category: Homeodomain]]
| + | |
| Structural highlights
Function
VND_DROME Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The interactions responsible for the nucleotide sequence-specific binding of the vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding site have been identified. A three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex is presented, with emphasis on the structure of regions of observed protein-DNA contacts. This structure is based on protein-DNA distance restraints derived from NMR data, along with homology modeling, solvated molecular dynamics, and results from methylation and ethylation interference experiments. Helix III of the homeodomain binds in the major groove of the DNA and the N-terminal arm binds in the minor groove, in analogy with other homeodomain-DNA complexes whose structures have been reported. The vnd/NK-2 homeodomain recognizes the unusual DNA consensus sequence 5'-CAAGTG-3'. The roles in sequence specificity and strength of binding of individual amino acid residues that make contact with the DNA are described. We show, based primarily on the observed protein-DNA contacts, that the interaction of Y54 with the DNA is the major determinant of this uncommon nucleotide binding specificity in the vnd/NK-2 homeodomain-DNA complex.
Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.,Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA Biochemistry. 1997 May 6;36(18):5372-80. PMID:9154919[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA. Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity. Biochemistry. 1997 May 6;36(18):5372-80. PMID:9154919 doi:10.1021/bi9620060
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