The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.
The alternative splicing of mRNA is a critical process in higher eukaryotes that generates substantial proteomic diversity. Many of the proteins that are essential to this process contain arginine/serine-rich (RS) domains. ZRANB2 is a widely-expressed and highly-conserved RS-domain protein that can regulate alternative splicing but lacks canonical RNA-binding domains. Instead, it contains 2 RanBP2-type zinc finger (ZnF) domains. We demonstrate that these ZnFs recognize ssRNA with high affinity and specificity. Each ZnF binds to a single AGGUAA motif and the 2 domains combine to recognize AGGUAA(N(x))AGGUAA double sites, suggesting that ZRANB2 regulates alternative splicing via a direct interaction with pre-mRNA at sites that resemble the consensus 5' splice site. We show using X-ray crystallography that recognition of an AGGUAA motif by a single ZnF is dominated by side-chain hydrogen bonds to the bases and formation of a guanine-tryptophan-guanine "ladder." A number of other human proteins that function in RNA processing also contain RanBP2 ZnFs in which the RNA-binding residues of ZRANB2 are conserved. The ZnFs of ZRANB2 therefore define another class of RNA-binding domain, advancing our understanding of RNA recognition and emphasizing the versatility of ZnF domains in molecular recognition.
Loughlin
Fionna E
FE
School of Molecular and Microbial Biosciences, University of Sydney, Sydney NSW 2006, Australia.
Mansfield
Robyn E
RE
Vaz
Paula M
PM
McGrath
Aaron P
AP
Setiyaputra
Surya
S
Gamsjaeger
Roland
R
Chen
Eva S
ES
Morris
Brian J
BJ
Guss
J Mitchell
JM
Mackay
Joel P
JP
D000595:Amino Acid Sequence; D001665:Binding Sites; D006801:Humans; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism*; D022821:RNA Splice Sites; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D016335:Zinc Fingers
D022821:RNA Splice Sites; D016601:RNA-Binding Proteins; C486373:ZRANB2 protein, human; D012313:RNA