title: Structural basis for the modular recognition of single-stranded RNA by PPR proteins.
abstract: Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants, recognize single-stranded RNA (ssRNA) in a modular fashion. The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI-ATPH and PSAJ-RPL33 intergenic regions, referred to as ATPH and PSAJ, respectively. By protecting the target RNA elements from 5' or 3' exonucleases, PPR10 defines the corresponding 5' and 3' messenger RNA termini. Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45 Å, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.
authors.affiliation: 1] State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China [2] Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China [3].
authors.forename: Ping
authors.initials: P
authors.lastname: Yin
authors.forename: Quanxiu
authors.initials: Q
authors.lastname: Li
authors.forename: Chuangye
authors.initials: C
authors.lastname: Yan
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Junjie
authors.initials: J
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Yu
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Jiafu
authors.initials: J
authors.lastname: Long
authors.forename: Jianhua
authors.initials: J
authors.lastname: He
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Wang
authors.forename: Jiawei
authors.initials: J
authors.lastname: Wang
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: Yigong
authors.initials: Y
authors.lastname: Shi
authors.forename: Nieng
authors.initials: N
authors.lastname: Yan
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D003313:Zea mays / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D012313:RNA