PDBsum entry: 3bsb

RNA binding protein/RNA

PDB id: 3bsb

Contents

Protein chains

340 a.a. *

DNA/RNA

Waters ×145

* Residue conservation analysis

PDB id:

3bsb

Name:

RNA binding protein/RNA

Title:

Crystal structure of human pumilio1 in complex with cyclinb reverse RNA

Structure:

Pumilio homolog 1. Chain: a, b. Fragment: pumilio-puf domain. Synonym: pumilio-1, hspum. Engineered: yes. 5'-r( Up Up Up Ap Ap Up Gp Up U)-3'. Chain: c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pum1, kiaa0099, pumh1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.80Å R-factor: 0.244 R-free: 0.268

Authors:

Y.K.Gupta,D.T.Nair,R.P.Wharton,A.K.Aggarwal

Key ref:

Y.K.Gupta et al. (2008). Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity. Structure, 16, 549-557. PubMed id: 18328718 DOI: 10.1016/j.str.2008.01.006

Date:

23-Dec-07 Release date: 08-Apr-08

Protein chains

Q14671  (PUM1_HUMAN) -  Pumilio homolog 1

Seq: 1186 a.a.

Struc: 340 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (2 terms)

DOI no: 10.1016/j.str.2008.01.006

Structure 16:549-557 (2008)

PubMed id: 18328718

Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

Y.K.Gupta, D.T.Nair, R.P.Wharton, A.K.Aggarwal.

ABSTRACT

Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycB(reverse) and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a "spacer." The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.

Selected figure(s)

Figure 3.
Figure 3. A Schematic of hPum-RNA Interactions
Schematic representations of hPum-RNA interactions in hb-NRE, CycB[reverse], and Puf5 structures. Hydrogen bonds are depicted as continuous single black dots (……) and distances are shown on the top of the dots. van der Waals contacts are shown by double dotted lines (:::::::), and stacking interactions by green arrows. The U[2] base in CycB[reverse] structure is shown in a dotted box because of its weak density and tentative contacts.

Figure 4.
Figure 4. Close-Up Views of Base Interactions
(A) An alignment of hb-NRE, CycB[reverse], and Puf5 RNA portions that bind the inner concave surface of hPum. Bases that differ are outlined with blue boxes. The flipped-out nucleotide U[6] is highlighted in red.
(B) Recognition of G (hb-NRE and Puf5) or U (CycB[reverse]) by Puf repeat 7.
(C) Recognition of A (hb-NRE) or U (CycB[reverse] and Puf5) by Puf repeat 1.
(D) Interactions with CA (hb-NRE), AUG (CycB[reverse]), or AUA (Puf5) by Puf repeats 5–3.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 549-557) copyright 2008.

Figures were selected by an automated process.