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| | <StructureSection load='5d23' size='340' side='right'caption='[[5d23]], [[Resolution|resolution]] 1.95Å' scene=''> | | <StructureSection load='5d23' size='340' side='right'caption='[[5d23]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5d23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bommo Bommo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D23 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5d23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bombyx_mori Bombyx mori] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D23 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d2s|5d2s]], [[5d2q|5d2q]]</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=5d23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d23 OCA], [https://pdbe.org/5d23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d23 RCSB], [https://www.ebi.ac.uk/pdbsum/5d23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d23 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fmbp-1, Fmbp-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7091 BOMMO])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5d23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d23 OCA], [http://pdbe.org/5d23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d23 RCSB], [http://www.ebi.ac.uk/pdbsum/5d23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d23 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5FBS0_BOMMO Q5FBS0_BOMMO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bommo]] | + | [[Category: Bombyx mori]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cheng, W]] | + | [[Category: Synthetic construct]] |
| - | [[Category: All a-helix]] | + | [[Category: Cheng W]] |
| - | [[Category: Major groove binding pattern]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Transcription-dna complex]]
| + | |
| Structural highlights
Function
Q5FBS0_BOMMO
Publication Abstract from PubMed
Despite over 3300 protein-DNA complex structures have been reported in the past decades, there remain some unknown recognition patterns between protein and target DNA. The silkgland-specific transcription factor FMBP-1 from the silkworm Bombyx mori contains a unique DNA-binding domain of four tandem STPRs, namely the score and three amino acid peptide repeats. Here we report three structures of this STPR domain (termed BmSTPR) in complex with DNA of various lengths. In the presence of target DNA, BmSTPR adopts a zig-zag structure of three or four tandem alpha-helices that run along the major groove of DNA. Structural analyses combined with binding assays indicate BmSTPR prefers the AT-rich sequences, with each alpha-helix covering a DNA sequence of 4 bp. The successive AT-rich DNAs adopt a wider major groove, which is in complementary in shape and size to the tandem alpha-helices of BmSTPR. Substitutions of DNA sequences and affinity comparison further prove that BmSTPR recognizes the major groove mainly via shape readout. Multiple-sequence alignment suggests this unique DNA-binding pattern should be highly conserved for the STPR domain containing proteins which are widespread in animals. Together, our findings provide structural insights into the specific interactions between a novel DNA-binding protein and a unique deformed B-DNA.
Structures of an all-alpha protein running along the DNA major groove.,Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ Nucleic Acids Res. 2016 May 5;44(8):3936-45. doi: 10.1093/nar/gkw133. Epub 2016, Mar 2. PMID:26939889[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ. Structures of an all-alpha protein running along the DNA major groove. Nucleic Acids Res. 2016 May 5;44(8):3936-45. doi: 10.1093/nar/gkw133. Epub 2016, Mar 2. PMID:26939889 doi:http://dx.doi.org/10.1093/nar/gkw133
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