4MJ7

Crystal structure of the PIN domain of Saccharomyces cerevisiae Utp23

Summary for 4MJ7

• Entry DOI: 10.2210/pdb4mj7/pdb
• Descriptor: rRNA-processing protein UTP23, ZINC ION (3 entities in total)
• Functional Keywords: pin domain, ribosome synthesis, 90s preribosome, nucleolus, rna binding protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Mitochondrion: Q12339
• Total number of polymer chains: 2
• Total formula weight: 36549.10

Authors

Lu, J.,Ye, K. (deposition date: 2013-09-03, release date: 2013-11-06, Last modification date: 2024-03-20)

Primary citation

Lu, J.,Sun, M.,Ye, K.
Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain
Rna, 19:1815-1824, 2013

PubMed Abstract: During synthesis of yeast ribosome, a large complex, called the 90S pre-ribosome or the small subunit processome, is assembled on the nascent precursor rRNA and mediates early processing of 18S rRNA. The Utp23 protein and snR30 H/ACA snoRNA are two conserved components of 90S pre-ribosomes. Utp23 contains a degenerate PIN nuclease domain followed by a long C-terminal tail and associates specifically with snR30. Here, we report the crystal structure of the Utp23 PIN domain at 2.5-Å resolution. The structure reveals a conserved core fold of PIN domain with degenerate active site residues, a unique CCHC Zn-finger motif, and two terminal extension elements. Functional sites of Utp23 have been examined with conservation analysis, mutagenesis, and in vivo and in vitro assays. Mutations in each of three cysteine ligands of zinc, although not the histidine ligand, were lethal or strongly inhibitory to yeast growth, indicating that the Zn-finger motif is required for Utp23 structure or function. The N-terminal helix extension harbors many highly conserved basic residues that mostly are critical for growth and in vitro RNA-binding activity of Utp23. Deletion of the C-terminal tail, which contains a short functionally important sequence motif, disrupted the interaction of Utp23 with snR30 and perturbed the pre-ribosomal association of Utp23. Our data establish a structural framework for dissecting Utp23 function in the assembly and dynamics of 90S pre-ribosomes.

PubMed: 24152547
DOI: 10.1261/rna.040808.113

Experimental method

X-RAY DIFFRACTION (2.51 Å)