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| | ==crystal structure of FBF-2/gld-1 FBEa A7U mutant complex== | | ==crystal structure of FBF-2/gld-1 FBEa A7U mutant complex== |
| - | <StructureSection load='3qg9' size='340' side='right' caption='[[3qg9]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='3qg9' size='340' side='right'caption='[[3qg9]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3qg9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QG9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QG9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3qg9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QG9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k5y|3k5y]], [[3qgb|3qgb]], [[3qgc|3qgc]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fbf-2, F21H12.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=3qg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qg9 OCA], [https://pdbe.org/3qg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qg9 RCSB], [https://www.ebi.ac.uk/pdbsum/3qg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qg9 ProSAT]</span></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=3qg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qg9 OCA], [http://pdbe.org/3qg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qg9 RCSB], [http://www.ebi.ac.uk/pdbsum/3qg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qg9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/FBF2_CAEEL FBF2_CAEEL]] Involved in the control of stem cells and sex determination in the C.elegans hermaphrodite germline. May also play a role in the hermaphrodite germline proliferation and oogenesis. Binds specifically to the regulatory region of fem-3 3'-UTR and mediates the sperm/oocyte switch. Negatively regulates gld-3 expression possibly by directly binding to two sites within the gld-3 isoform B 3'-UTR.<ref>PMID:9393998</ref> <ref>PMID:15454534</ref> | + | [https://www.uniprot.org/uniprot/FBF2_CAEEL FBF2_CAEEL] Involved in the control of stem cells and sex determination in the C.elegans hermaphrodite germline. May also play a role in the hermaphrodite germline proliferation and oogenesis. Binds specifically to the regulatory region of fem-3 3'-UTR and mediates the sperm/oocyte switch. Negatively regulates gld-3 expression possibly by directly binding to two sites within the gld-3 isoform B 3'-UTR.<ref>PMID:9393998</ref> <ref>PMID:15454534</ref> |
| | <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: Caeel]] | + | [[Category: Caenorhabditis elegans]] |
| - | [[Category: Gross, L]] | + | [[Category: Large Structures]] |
| - | [[Category: Hall, T M.T]] | + | [[Category: Gross L]] |
| - | [[Category: Koh, Y Y]] | + | [[Category: Hall TMT]] |
| - | [[Category: Opperman, L]] | + | [[Category: Koh YY]] |
| - | [[Category: Qiu, C]] | + | [[Category: Opperman L]] |
| - | [[Category: Wang, Y]] | + | [[Category: Qiu C]] |
| - | [[Category: Wickens, M]] | + | [[Category: Wang Y]] |
| - | [[Category: Puf repeat]]
| + | [[Category: Wickens M]] |
| - | [[Category: Rna binding domain]]
| + | |
| - | [[Category: Rna binding protein-rna complex]]
| + | |
| Structural highlights
Function
FBF2_CAEEL Involved in the control of stem cells and sex determination in the C.elegans hermaphrodite germline. May also play a role in the hermaphrodite germline proliferation and oogenesis. Binds specifically to the regulatory region of fem-3 3'-UTR and mediates the sperm/oocyte switch. Negatively regulates gld-3 expression possibly by directly binding to two sites within the gld-3 isoform B 3'-UTR.[1] [2]
Publication Abstract from PubMed
Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to "target" versus "off-target" interactions, and thus be an important consideration in the design of proteins with new specificities.
Stacking interactions in PUF-RNA complexes.,Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall TM, Wickens M RNA. 2011 Apr;17(4):718-27. Epub 2011 Mar 3. PMID:21372189[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhang B, Gallegos M, Puoti A, Durkin E, Fields S, Kimble J, Wickens MP. A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature. 1997 Dec 4;390(6659):477-84. PMID:9393998 doi:10.1038/37297
- ↑ Eckmann CR, Crittenden SL, Suh N, Kimble J. GLD-3 and control of the mitosis/meiosis decision in the germline of Caenorhabditis elegans. Genetics. 2004 Sep;168(1):147-60. PMID:15454534 doi:10.1534/genetics.104.029264
- ↑ Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall TM, Wickens M. Stacking interactions in PUF-RNA complexes. RNA. 2011 Apr;17(4):718-27. Epub 2011 Mar 3. PMID:21372189 doi:10.1261/rna.2540311
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