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The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.

Tan D, Zhou M, Kiledjian M, Tong L - Nat. Struct. Mol. Biol. (2014)

Bottom Line: The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III.The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II.Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site).

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Columbia University, New York, New York, USA.

ABSTRACT
A conserved stem-loop motif of the constitutive decay element (CDE) in the 3' UTR of mRNAs is recognized by the ROQ domain of Roquin, which mediates mRNA degradation. Here we report two crystal structures of the Homo sapiens ROQ domain in complex with CDE RNA. The ROQ domain has an elongated shape with three subdomains. The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III. The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II. Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site). Mutation in either site perturbs the Roquin-mediated degradation of HMGXB3 and IL6 mRNAs in human cells, demonstrating the importance of both sites for mRNA decay.

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Structure of the ROQ domain of human Roquin in complex with the CDE of TNF-α mRNA(a). Two views of the structure of the ROQ domain of human Roquin in complex with the TNF23 RNA. Only half of the TNF23 RNA duplex is shown. (b). Overview of the interface between TNF23 RNA (orange) and the ROQ domain (yellow and cyan). (c). Interactions between the 5′ arm of TNF23 and domain II of the ROQ domain. Water molecules are shown as red spheres. (d). Interactions between the 3′ arm of TNF23 and domain I of the ROQ domain
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Figure 3: Structure of the ROQ domain of human Roquin in complex with the CDE of TNF-α mRNA(a). Two views of the structure of the ROQ domain of human Roquin in complex with the TNF23 RNA. Only half of the TNF23 RNA duplex is shown. (b). Overview of the interface between TNF23 RNA (orange) and the ROQ domain (yellow and cyan). (c). Interactions between the 5′ arm of TNF23 and domain II of the ROQ domain. Water molecules are shown as red spheres. (d). Interactions between the 3′ arm of TNF23 and domain I of the ROQ domain

Mentions: The TNF23 duplex contains six Watson-Crick base pairs from each of the stem regions of the TNF23 RNA (Supplementary Fig. 5). The two ROQ domains in the asymmetric unit have contacts with the base-paired regions of the TNF23 RNA but have no interactions with the nucleotides in the loop region in the middle of the duplex (Supplementary Fig. 5). The RNA is positioned in an electropositive surface depression at the interface of domains I and II (Supplementary Fig. 4), and we will refer to this binding site as the B site (Fig. 3a).


The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.

Tan D, Zhou M, Kiledjian M, Tong L - Nat. Struct. Mol. Biol. (2014)

Structure of the ROQ domain of human Roquin in complex with the CDE of TNF-α mRNA(a). Two views of the structure of the ROQ domain of human Roquin in complex with the TNF23 RNA. Only half of the TNF23 RNA duplex is shown. (b). Overview of the interface between TNF23 RNA (orange) and the ROQ domain (yellow and cyan). (c). Interactions between the 5′ arm of TNF23 and domain II of the ROQ domain. Water molecules are shown as red spheres. (d). Interactions between the 3′ arm of TNF23 and domain I of the ROQ domain
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4125485&req=5

Figure 3: Structure of the ROQ domain of human Roquin in complex with the CDE of TNF-α mRNA(a). Two views of the structure of the ROQ domain of human Roquin in complex with the TNF23 RNA. Only half of the TNF23 RNA duplex is shown. (b). Overview of the interface between TNF23 RNA (orange) and the ROQ domain (yellow and cyan). (c). Interactions between the 5′ arm of TNF23 and domain II of the ROQ domain. Water molecules are shown as red spheres. (d). Interactions between the 3′ arm of TNF23 and domain I of the ROQ domain
Mentions: The TNF23 duplex contains six Watson-Crick base pairs from each of the stem regions of the TNF23 RNA (Supplementary Fig. 5). The two ROQ domains in the asymmetric unit have contacts with the base-paired regions of the TNF23 RNA but have no interactions with the nucleotides in the loop region in the middle of the duplex (Supplementary Fig. 5). The RNA is positioned in an electropositive surface depression at the interface of domains I and II (Supplementary Fig. 4), and we will refer to this binding site as the B site (Fig. 3a).

Bottom Line: The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III.The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II.Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site).

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Columbia University, New York, New York, USA.

ABSTRACT
A conserved stem-loop motif of the constitutive decay element (CDE) in the 3' UTR of mRNAs is recognized by the ROQ domain of Roquin, which mediates mRNA degradation. Here we report two crystal structures of the Homo sapiens ROQ domain in complex with CDE RNA. The ROQ domain has an elongated shape with three subdomains. The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III. The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II. Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site). Mutation in either site perturbs the Roquin-mediated degradation of HMGXB3 and IL6 mRNAs in human cells, demonstrating the importance of both sites for mRNA decay.

Show MeSH
Related in: MedlinePlus