6l8u | pdb_00006l8u
Crystal structure of human BCDIN3D in complex with SAH
Structural highlights
Function[BN3D2_HUMAN] O-methyltransferase that specifically monomethylates 5'-monophosphate of cytoplasmic histidyl tRNA, acting as a capping enzyme (PubMed:28119416). Less efficiently, also methylates the 5' monophosphate of pre-miRNAs, acting as a negative regulator of miRNA processing (PubMed:23063121, PubMed:28119416). The 5' monophosphate of pre-miRNAs is recognized by DICER1 and is required for pre-miRNAs processing: methylation at this position reduces the processing of pre-miRNAs by DICER1. Able to mediate methylation of pre-miR-145, as well as other pre-miRNAs (PubMed:23063121). There is some controversy about the methylation of pre-miR-145, since the dimethylation first described as the specific enzymatic activity cannot be reproduced by a more recent work which observes a monomehtylation of pre-miR-145 but two orders weaker than the methylation of cytosolic histidyl tRNA (PubMed:23063121, PubMed:28119416, PubMed:30127802).[1] [2] [3] Publication Abstract from PubMedBCDIN3 domain containing RNA methyltransferase, BCDIN3D, monomethylates the 5'-monophosphate of cytoplasmic tRNAHis with a G-1:A73 mispair at the top of an eight-nucleotide-long acceptor helix, using S-adenosyl-l-methionine (SAM) as a methyl group donor. In humans, BCDIN3D overexpression is associated with the tumorigenic phenotype and poor prognosis in breast cancer. Here, we present the crystal structure of human BCDIN3D complexed with S-adenosyl-l-homocysteine. BCDIN3D adopts a classical Rossmann-fold methyltransferase structure. A comparison of the structure with that of the closely related methylphosphate capping enzyme, MePCE, which monomethylates the 5'-gamma-phosphate of 7SK RNA, revealed the important residues for monomethyl transfer from SAM onto the 5'-monophosphate of tRNAHis and for tRNAHis recognition by BCDIN3D. A structural model of tRNAHis docking onto BCDIN3D suggested the molecular mechanism underlying the different activities between BCDIN3D and MePCE. A loop in BCDIN3D is shorter, as compared to the corresponding region that forms an alpha-helix to recognize the 5'-end of RNA in MePCE, and the G-1:A73 mispair in tRNAHis allows the N-terminal alpha-helix of BCDIN3D to wedge the G-1:A73 mispair of tRNAHis. As a result, the 5'-monophosphate of G-1 of tRNAHis is deep in the catalytic pocket for 5'-phosphate methylation. Thus, BCDIN3D is a tRNAHis-specific 5'-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers. Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.,Liu Y, Martinez A, Yamashita S, Tomita K Nucleic Acids Res. 2020 Jan 10. pii: 5699672. doi: 10.1093/nar/gkz1216. PMID:31919512[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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