Rde 4 sandbox
From Proteopedia
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==Introduction== | ==Introduction== | ||
| - | RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA- binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. RDE-4 is a homodimer in solution. (Yellow | + | RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA- binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. <ref>DOI: 10.1042/BJ20131347</ref> (Yellow Citation) |
<Structure load='2LTR' size='350' frame='true' align='right' caption='Structure of RDE-4 (pdb code 2LTR) scene='Insert optional scene name here' /> | <Structure load='2LTR' size='350' frame='true' align='right' caption='Structure of RDE-4 (pdb code 2LTR) scene='Insert optional scene name here' /> | ||
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
| - | == | + | == Structure of RDE-4 == |
| + | RDE-4 has five major regions: an N-terminal region (residues 1–43), two dsRBDs (residues 44–108 and 170–235), a long linker (residues 109–169) and a C-terminal domain (residues 236–385). Amino acid residues 1–32 and 136–151 adopt a random coiled structure and do not make any contact within itself or with the rest of the structure. Parts of the linker, residues 109–135 and 152–169, assume an α-helix and an extended loop structure, respectively. There is not any long-range nuclear Overhauser effect information between regions 1–135 and 152– 243, suggesting that the unstructured part of the linker 136–151 separates both of these regions. The region encompassed by 236–243 folds into an α-helix. The amino acid regions 44–108 and 170–235 form dsRBD1 and dsRBD2, respectively. The hydrophobic residues Leu45, Val47, Leu48, Val55, Trp62, Met73, Leu75, Leu77, Ile80, Val82, Leu101, and Val105 stabilize dsRBD1, and Val171, Leu174, Leu183, Val201, Met205, Met227, and Leu232 form the core of dsRBD2. Apart from the canonical dsRBD fold, there are additional secondary-structural elements that are observed in both RDE-4D1 and RDE-4D2. (Purple citation) | ||
| + | == Function == | ||
| - | == Structure of RDE-4 == | ||
| - | |||
| - | RDE-4 has five major regions: an N-terminal region (residues 1–43), two dsRBDs (residues 44–108 and 170–235), a long linker (residues 109–169) and a C-terminal domain (residues 236–385). Amino acid residues 1–32 and 136–151 adopt a random coiled structure and do not make any contact within itself or with the rest of the structure. Parts of the linker, residues 109–135 and 152–169, assume an α-helix and an extended loop structure, respectively. There is not any long-range nuclear Overhauser effect information between regions 1–135 and 152– 243, suggesting that the unstructured part of the linker 136–151 separates both of these regions. The region encompassed by 236–243 folds into an α-helix. The amino acid regions 44–108 and 170–235 form dsRBD1 and dsRBD2, respectively. The hydrophobic residues Leu45, Val47, Leu48, Val55, Trp62, Met73, Leu75, Leu77, Ile80, Val82, Leu101, and Val105 stabilize dsRBD1, and Val171, Leu174, Leu183, Val201, Met205, Met227, and Leu232 form the core of dsRBD2. Apart from the canonical dsRBD fold, there are additional secondary-structural elements that are observed in both RDE-4D1 and RDE-4D2. (Purple citation) | ||
Revision as of 00:44, 9 October 2018
Contents |
Introduction
RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA- binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. [1] (Yellow Citation)
|
You may include any references to papers as in: the use of JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.
Structure of RDE-4
RDE-4 has five major regions: an N-terminal region (residues 1–43), two dsRBDs (residues 44–108 and 170–235), a long linker (residues 109–169) and a C-terminal domain (residues 236–385). Amino acid residues 1–32 and 136–151 adopt a random coiled structure and do not make any contact within itself or with the rest of the structure. Parts of the linker, residues 109–135 and 152–169, assume an α-helix and an extended loop structure, respectively. There is not any long-range nuclear Overhauser effect information between regions 1–135 and 152– 243, suggesting that the unstructured part of the linker 136–151 separates both of these regions. The region encompassed by 236–243 folds into an α-helix. The amino acid regions 44–108 and 170–235 form dsRBD1 and dsRBD2, respectively. The hydrophobic residues Leu45, Val47, Leu48, Val55, Trp62, Met73, Leu75, Leu77, Ile80, Val82, Leu101, and Val105 stabilize dsRBD1, and Val171, Leu174, Leu183, Val201, Met205, Met227, and Leu232 form the core of dsRBD2. Apart from the canonical dsRBD fold, there are additional secondary-structural elements that are observed in both RDE-4D1 and RDE-4D2. (Purple citation)
Function
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</StructureSection>
References
- ↑ Chiliveri SC, Deshmukh MV. Structure of RDE-4 dsRBDs and mutational studies provide insights in the dsRNA recognition in C. elegans RNAi pathway. Biochem J. 2013 Nov 21. PMID:24256178 doi:http://dx.doi.org/10.1042/BJ20131347
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
