PDBsum entry 3k49

RNA binding protein / RNA

PDB id: 3k49

Contents

Protein chains

353 a.a. *

DNA/RNA

Ligands

CIT ×3

Waters ×431

* Residue conservation analysis

PDB id:

3k49

Name:

RNA binding protein / RNA

Title:

Puf3 RNA binding domain bound to cox17 RNA 3' utr recognition sequence site b

Structure:

mRNA-binding protein puf3. Chain: a, c, e. Fragment: residues 511-879. Synonym: pumilio homology domain family member 3. Engineered: yes. RNA (5'-r( Cp Cp Up Gp Up Ap Ap Ap Up A)-3'). Chain: b, d, f. Engineered: yes. Other_details: cox17 site b

Source:

Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: l1325, puf3, yll013c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: RNA oligonucleotides were obtained from dharmacon, inc.

Resolution:

2.50Å R-factor: 0.230 R-free: 0.263

Authors:

D.Zhu,C.R.Stumpf,J.M.Krahn,M.Wickens,T.M.T.Hall

Key ref:

D.Zhu et al. (2009). A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs. Proc Natl Acad Sci U S A, 106, 20192-20197. PubMed id: 19918084

Date:

05-Oct-09 Release date: 27-Oct-09

Protein chains

Q07807  (PUF3_YEAST) -  mRNA-binding protein PUF3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 879 a.a.

Struc: 353 a.a.

DNA/RNA chains

C-C-U-G-U-A-A-A-U-A 10 bases

C-C-U-G-U-A-A-A-U-A 10 bases

C-C-U-G-U-A-A-A-U-A 10 bases

Proc Natl Acad Sci U S A 106:20192-20197 (2009)

PubMed id: 19918084

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.

D.Zhu, C.R.Stumpf, J.M.Krahn, M.Wickens, T.M.Hall.

ABSTRACT

A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity. To do so, we explore the crystal structures of Puf3p complexes with 2 cognate RNAs. The key determinant of Puf3p specificity is an unusual interaction between a distinctive pocket of the protein with an RNA base outside the "core" PUF-binding site. That interaction dramatically affects binding affinity in vitro and is required for regulation in vivo. The Puf3p structures, combined with those of Puf4p in the same organism, illuminate the structural basis of natural PUF-RNA networks. Yeast Puf3p binds its own RNAs because they possess a -2C and is excluded from those of Puf4p which contain an additional nucleotide in the core-binding site.