PDBsum entry: 1m8z

RNA binding protein

PDB id: 1m8z

Contents

Protein chain

339 a.a. *

Ligands

BME

Waters ×406

* Residue conservation analysis

PDB id:

1m8z

Name:

RNA binding protein

Title:

Crystal structure of a pumilio-homology domain

Structure:

Pumilio 1. Chain: a. Fragment: pumilio-homology domain (residues 828-1176). Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PDB file)

Resolution:

1.90Å R-factor: 0.194 R-free: 0.242

Authors:

X.Wang,P.D.Zamore,T.M.T.Hall

Key ref:

X.Wang et al. (2001). Crystal structure of a Pumilio homology domain. Mol Cell, 7, 855-865. PubMed id: 11336708 DOI: 10.1016/S1097-2765(01)00229-5

Date:

26-Jul-02 Release date: 04-Sep-02

Supersedes:

1ib3

Protein chain

Q14671  (PUM1_HUMAN) -  Pumilio homolog 1

Seq: 1186 a.a.

Struc: 339 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (2 terms)

DOI no: 10.1016/S1097-2765(01)00229-5

Mol Cell 7:855-865 (2001)

PubMed id: 11336708

Crystal structure of a Pumilio homology domain.

X.Wang, P.D.Zamore, T.M.Hall.

ABSTRACT

Puf proteins regulate translation and mRNA stability by binding sequences in their target RNAs through the Pumilio homology domain (PUM-HD), which is characterized by eight tandem copies of a 36 amino acid motif, the PUM repeat. We have solved the structure of the PUM-HD from human Pumilio1 at 1.9 A resolution. The structure reveals that the eight PUM repeats correspond to eight copies of a single, repeated structural motif. The PUM repeats pack together to form a right-handed superhelix that approximates a half doughnut. The distribution of side chains on the inner and outer faces of this half doughnut suggests that the inner face of the PUM-HD binds RNA while the outer face interacts with proteins such as Nanos, Brain Tumor, and cytoplasmic polyadenylation element binding protein.

Selected figure(s)

Figure 1.
Figure 1. Structure of a Human Pumilio Homology Domain(A) Ribbon diagram of the HsPUM-HD. Residues Gly-828 to Ala-1162 are shown. Residues Lys-1150 to Ala-1162 are shown with dashed lines and are lighter in color. Repeats are colored alternately blue and yellow. The N and C termini are indicated. The loop containing Gly-1107 to His-1109 is colored red.(B) Structural alignment of the PUM-HD repeats. Repeats 2–8 were aligned with respect to repeat 1. Repeats 1–8 are colored sequentially: 1, blue; 2, green; 3, yellow; 4, red; 5, magenta; 6, cyan; 7, orange; 8, purple. The N and C termini are indicated. This figure was prepared with the program MOLSCRIPT (Kraulis, 1991)

Figure 4.
Figure 4. Possible PUM-HD RNA and Protein Interaction Surfaces(A) Electrostatic surface representation of the HsPUM-HD. The molecule is rotated approximately 90° about the vertical axis with respect to Figure 1A and shows the concave surface proposed to bind RNA. Blue represents regions of positive potential and red represents regions of negative potential at the 10 kT/e level.(B) Electrostatic surface representation as in (A), but rotated 180° about the vertical axis relative to (A) to show the convex surface proposed to interact with NOS, BRAT, or CPEB.(C) Stereo ribbon diagram of the HsPUM-HD showing the side chains that lie on the proposed RNA binding and protein binding surfaces. Side chains on the concave surface are colored as in Figure 2B. Acidic side chains (Asp and Glu) in α1 and α3 are colored red. Side chains corresponding to the location of mutations in DmPUM are colored green. The protein is oriented as in Figure 1A.(D) Molecular surface representation as in (B), but rotated 60° about the horizontal axis with respect to (B) to show the proposed NOS- and BRAT-interacting surfaces. Indicated on the HsPUM-HD are the positions of mutations in DmPUM that disrupt interaction with BRAT (pink), the loop in HsPUM that blocks its interaction with NOS in flies and that corresponds to the MluI insertion in DmPUM (green), and sites of mutations that disrupt neither DmPUM function nor BRAT binding (black). Mutation positions are numbered according to the sequence of DmPUM, not HsPUM. The position of the DmPUM^680 mutation corresponds to HsPUM Gly-1067, DmPUM Cys-1365 to HsPUM Cys-1102, and DmPUM Thr-1366 to HsPUM Thr-1103. Likewise, DmPUM Gly-1186 is HsPUM Gly-923, Gly-1222 is Gly-959, Gly-1258 is Gly-995, and Lys-1331 corresponds to Asn-1068. (A, B, and D) were prepared with the program GRASP (Nicholls et al., 1991). (C) was prepared with MOLSCRIPT (Kraulis, 1991)

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 7, 855-865) copyright 2001.

Figures were selected by the author.