Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition

Abstract

Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome. The zinc-finger motif was discovered during biochemical studies on the transcription factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis. Zinc-fingers mostly interact with DNA, but TFIIIA binds not only specifically to the promoter DNA, but also to 5S RNA itself. Increasing evidence indicates that zinc-fingers are more widely used to recognize RNA. There have been numerous structural studies on DNA binding, but none on RNA binding by zinc-finger proteins. Here we report the crystal structure of a three-finger complex with 61 bases of RNA, derived from the central regions of the complete nine-finger TFIIIA-5S RNA complex. The structure reveals two modes of zinc-finger binding, both of which differ from that in common use for DNA: first, the zinc-fingers interact with the backbone of a double helix; and second, the zinc-fingers specifically recognize individual bases positioned for access in otherwise intricately folded 'loop' regions of the RNA.

The Hantavirus Glycoprotein G1 Tail Contains Dual CCHC-type Classical Zinc Fingers

“…Classical zinc fingers are well known DNA-and RNAbinding domains (17,18,44). Recent reports indicate that proteins containing classical zinc fingers are also involved in protein-protein interaction (43,(45)(46)(47).…”

“…Commonly, classical zinc fingers fold independently of each other, forming a beads-on-a-string configuration. However, multiple classical zinc fingers can interact with each other when bound to DNA (44) or RNA (17,18). Another example of a dual classical ␤␤␣ zinc finger that folds together as one unit is the yeast Zap1 transcription factor (49).…”

“…Further, this region was predicted to form a RING finger motif in the G1 tail of hantavirus (14). Here, we show by NMR that the conserved cysteine/ histidine region in the G1 tail of hantaviruses forms two classical ␤␤␣-fold zinc fingers (15)(16)(17)(18) and not a RING finger structure as suggested earlier (14). We also discuss the implication of our structural findings of the hantavirus G1 tail in the context of viral assembly and host pathogen interaction.…”

The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5′ splice site-like sequences

“…In both cases, each ZnF recognizes ssRNA in a sequence-specific manner with micromolar affinity and there does not appear to be a requirement for the RNA to be presented in a specific conformation. In contrast, a number of other RNA-binding proteins, including Nova (27), RBMY (28), nucleolin (29), TFIIIA (30), and the nucleocapsid ZnFs (23), recognize RNA in the context of a specific secondary structure. The presence of 2 (or more) modular RNA-binding domains that recognize a single RNA sequence is also a common theme in nucleic acid recognition (31), and one that potentially allows double sites with variable spacing to be recognized.…”

Zinc fingers are known as domains for binding DNA and RNA. Do they also mediate protein-protein interactions?

“…Work from several groups revealed that tandem arrays of three or more of these zinc fingers could recognize DNA in a sequence-specific manner by means of the helical region in each ZnF (3), and this became the paradigm for ZnF function. It has also been shown that some classical ZnFs can recognize RNA, an observation for which structural confirmation was presented recently (4,5).…”