PDBsum entry: 3bx2

Transcription, RNA binding protein/RNA

PDB id: 3bx2

Contents

Protein chains

328 a.a. *

DNA/RNA

Ligands

SO4 ×8

Metals

_NA ×2

Waters ×58

* Residue conservation analysis

PDB id:

3bx2

Name:

Transcription, RNA binding protein/RNA

Title:

Puf4 RNA binding domain bound to ho endonuclease RNA 3' utr recognition sequence

Structure:

Protein puf4. Chain: a, b. Fragment: single stranded RNA binding domin. Engineered: yes. Ho endonuclease 3' utr binding sequence. Chain: c, d. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: puf4. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.84Å R-factor: 0.240 R-free: 0.280

Authors:

M.T.Miller,J.J.Higgin,T.M.T.Hall

Key ref:

M.T.Miller et al. (2008). Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nat Struct Mol Biol, 15, 397-402. PubMed id: 18327269 DOI: 10.1038/nsmb.1390

Date:

11-Jan-08 Release date: 11-Mar-08

Protein chains

P25339  (PUF4_YEAST) -  Pumilio homology domain family member 4

Seq: 888 a.a.

Struc: 328 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (2 terms)

DOI no: 10.1038/nsmb.1390

Nat Struct Mol Biol 15:397-402 (2008)

PubMed id: 18327269

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p.

M.T.Miller, J.J.Higgin, T.M.Hall.

ABSTRACT

Pumilio/FBF (PUF) family proteins are found in eukaryotic organisms and regulate gene expression post-transcriptionally by binding to sequences in the 3' untranslated region of target transcripts. PUF proteins contain an RNA binding domain that typically comprises eight alpha-helical repeats, each of which recognizes one RNA base. Some PUF proteins, including yeast Puf4p, have altered RNA binding specificity and use their eight repeats to bind to RNA sequences with nine or ten bases. Here we report the crystal structures of Puf4p alone and in complex with a 9-nucleotide (nt) target RNA sequence, revealing that Puf4p accommodates an 'extra' nucleotide by modest adaptations allowing one base to be turned away from the RNA binding surface. Using structural information and sequence comparisons, we created a mutant Puf4p protein that preferentially binds to an 8-nt target RNA sequence over a 9-nt sequence and restores binding of each protein repeat to one RNA base.

Selected figure(s)

Figure 2.
(a) Schematic representation of the interaction between Puf4p and HO RNA. Distances (Å) between interacting atoms are indicated; (b) Puf4p recognition of the 5' conserved UGUA sequence (U1–A4). The protein and RNA in b–d are colored as in Figure 1a. (c) Puf4p recognition of the 3' conserved UA sequence (U8–A9). (d) Puf4p recognition of the central UAU sequence (U5–U7). The carbon atoms in U7 are colored yellow.

Figure 3.
(a) Interaction of repeats 3–5 of the T650C C724R mutPuf4p with cox17 Puf3 target RNA fragment (UGUAUAUA). Protein repeats are colored alternately blue and green. The RNA is colored as in Figure 1a, except that carbon atoms are colored tan. Cys650 and Arg724 are shown in yellow. (b) Interaction of repeats 3–5 of PUM1 with NRE RNA. Cys935 and Arg1008 are equivalent to Cys650 and Arg724 in mutPuf4p.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 397-402) copyright 2008.

Figures were selected by the author.