A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer.
We have solved two families of crystal structures of the human Dicer "platform-PAZ-connector helix" cassette in complex with small interfering RNAs (siRNAs). The structures possess two adjacently positioned pockets: a 2 nt 3'-overhang-binding pocket within the PAZ domain (3' pocket) and a phosphate-binding pocket within the platform domain (phosphate pocket). One family of complexes contains a knob-like α-helical protrusion, designated "hDicer-specific helix," that separates the two pockets and orients the bound siRNA away from the surface of Dicer, which could be indicative of a product release/transfer state. In the second complex, the helical protrusion is melted/disordered and the bound siRNA is aligned toward the surface of Dicer, suggestive of a cleavage-competent state. These structures allow us to propose that the transition from the cleavage-competent to the postulated product release/transfer state may involve release of the 5'-phosphate from the phosphate pocket while retaining the 3' overhang in the 3' pocket.
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Yuan
Y
Tian
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Dhirendra K
DK
Simanshu
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China.
Jin-Biao
JB
Ma
Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
Jong-Eun
JE
Park
School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
Inha
I
Heo
Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
V Narry
VN
Kim
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.
Dinshaw J
DJ
Patel
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D018360:Crystallography, X-Ray; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D051379:Mice; D018345:Mice, Knockout; D008969:Molecular Sequence Data; D009154:Mutation; D010710:Phosphates / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D034741:RNA, Small Interfering / Q000378:metabolism; D043244:Ribonuclease III / Q000737:chemistry* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D020349:Surface Plasmon Resonance
D010710:Phosphates; D034741:RNA, Small Interfering; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases