PDBsum entry: 1koo

RNA binding protein

PDB id: 1koo

Contents

Protein chains

258 a.a. *

165 a.a. *

* Residue conservation analysis

PDB id:

1koo

Name:

RNA binding protein

Title:

The crystal structure and mutational analysis of a novel RNA-binding domain found in the human tap nuclear mRNA export factor

Structure:

Tip associating protein. Chain: a, b, c, d. Fragment: residues 96-372. Synonym: tap. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.80Å R-factor: 0.317 R-free: 0.395

Authors:

D.N.Ho,G.A.Coburn,Y.Kang,B.R.Cullen,M.M.Georgiadis

Key ref:

D.N.Ho et al. (2002). The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. Proc Natl Acad Sci U S A, 99, 1888-1893. PubMed id: 11854490 DOI: 10.1073/pnas.042698599

Date:

21-Dec-01 Release date: 27-Feb-02

Protein chains

Q9UBU9  (NXF1_HUMAN) -  Nuclear RNA export factor 1

Seq: 619 a.a.

Struc: 258 a.a.*

Protein chains

Q9UBU9  (NXF1_HUMAN) -  Nuclear RNA export factor 1

Seq: 619 a.a.

Struc: 165 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: mRNA export from nucleus (1 term)
• Biochemical function: nucleotide binding (3 terms)

DOI no: 10.1073/pnas.042698599

Proc Natl Acad Sci U S A 99:1888-1893 (2002)

PubMed id: 11854490

The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor.

D.N.Ho, G.A.Coburn, Y.Kang, B.R.Cullen, M.M.Georgiadis.

ABSTRACT

The Tap protein mediates the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element (CTE). Previously, the structures of individual Tap subdomains, including ribonucleoprotein and leucine-rich repeat domains, have been described. Here, we report the crystal structure of a functional CTE RNA-binding domain of human Tap, including the N-terminal arm of the ribonucleoprotein domain and interdomain linking polypeptide. To identify residues that interact with the CTE, we have introduced 38 alanine substitutions for surface residues in the Tap CTE-binding domain and tested these mutants for their ability to support CTE-dependent nuclear RNA export and CTE binding. Four residues that cluster on a concave surface in the leucine-rich repeat domain were found to be critical for CTE binding and define a CTE-interacting surface on this domain. The second critical CTE-interacting surface on Tap is defined by three previously identified residues on the surface of the ribonucleoprotein domain. The structural and mutational data define a novel RNA-binding site on the Tap protein.

Selected figure(s)

Figure 3.
Fig. 3. The residues required for interactions of Tap with the CTE cluster on the surface of the RNP and LRR domains. (A) A surface representation is shown of the RNA-binding domain of Tap (96-372). Residues that do not affect binding are shown in green (see Results and Discussion). Residues that are important for binding are shown in red including R128, K129, K132, R233, R276, Y278, and K304. R249, which was reported (17) to be critical in binding, is shown in yellow. (B) The same surface representation of Tap as in A is shown rotated by approximately 180°.

Figure 4.
Fig. 4. Comparison of the RNA-interacting regions of Tap with those found in the U2B''-U2A'-RNA complex. (A) The Tap protein (96-372) is shown as a yellow ribbon rendering. The 1- and 3-strands of the RNP fold are shown as magenta arrows for comparison with the spliceosomal complex shown in B. Residues in the RNP and LRR domains of Tap that are critical for CTE binding (R128, K129, K132, R233, R249, R276, Y278, and K304) are shown as red balls and sticks. (B) A ribbon rendering of the structurally analogous spliceosomal complex including an RNP domain (U2B'') in yellow and LRR domain (U2A') in orange and a blue stick model of the hairpin fragment of U2 RNA as reported in the crystal structure (PDB ID code 1A9N) is shown. The same strands, 1 and 3, which include the residues of the RNP motifs (RNP2 and RNP1), are shown in magenta for comparison with Tap. The RNA-interacting surfaces of U2B'' and U2A' are clearly distinct from the CTE-interacting surfaces in Tap identified in our mutational analysis.

Figures were selected by an automated process.