RSS

PDB:2RIO

Protein Name

Inositol-requiring protein-1

Species

Yeast

Biological Context

In eukaryotic cells, most secreted and transmembrane proteins are modified and refold in the lumen of the endoplasmic reticulum(ER). The mature proteins which could fold into correct structure are coated by transport vesicles and delivered to the secretion pathway of the Golgi apparatus.(Refer to the PDB:2PM7 for the details).On the other hand, misfolded proteins which could not fold into correct structure are accumulated as defectives in the ER lumen. This situation is termed the ER stress. ER shows mainly three responses to the ER stress. (Fig.1).

1 (Fig.1) The three major responses to ER stress

(1) ERAD : ER Associated Degradation
Misfolded proteins are removed from the ER into the cytoplasm where they are degraded by the ubiquitin proteasome system.
(Refer to the PDB:2QYU for the details).

(2) UPR : Unfolded Protein Response
This is the pathway to decrease misfold proteins in the ER lumen. This pathway activates the regulation of protein translation and the production of chaperone proteins which assist protein folding.

(3) Induction of Apoptosis
If ER stress continued for a certain period, programmed cell death is triggered. This response has close relation to neurodegenerative disease or cancer. (1)ERAD or (2)UPR can be regarded as a mean which prevents from adopting this worst scenario.

So far, three different classes of ER stress transducer protein have been identified in (2)UPR pathway.

  • Inositol-requiring protein-1 (Ire1)
  • Activating transcription factor-6 (ATF6)
  • PKR-related ER kinase (PERK)

Each of them are ER-transmembrane protein that consists of a ER lumen part and a cytoplasm part: each part is located at inside and outside of the ER-membrane respectively. Although these three types of transducer protein recognize the misfold protein as a common input, their output signals are different. For instance, Ire1 outputs a signal which promotes splicing reaction of XBP1 mRNA. The crystal structure of Ire1 ER lumen part has already been determined. And it was turned out that Ire1 dimerizes into the active state in response to the misfold proteins. However, how Ire1 cytoplasm part dimerizes or the manner in which Ire1 removes intron remains unclear. For understanding these mechanisms, the crystal structure of Ire1 cytoplasm part has been determined.

2 (Fig.2) The role of Ire1 in UPR pathway

Ire1 ER lumen part detects elevated misfolded proteins in the ER and dimerizes into the active state. The cytoplasm part of active state Ire1 promotes XBP1 mRNA splicing reaction by removing intron from the precursor XBP1 mRNA which encode XBP1 protein. Then, mature XBP1 mRNA is translated into XBP1 protein. In turn, XBP1 protein upregulate the expression of the chaperone proteins or ERAD involving proteins in the nucleus.

Structure Description

2rio2rio_x2rio_y

The crystal structure of Ire1 dimer was determined at 2.4Å resolution. (Fig.3). Each protomer is consists of an N-terminal kinase domain and a C-terminal KEN domain(Kinase-Extension Nuclease domain). Furthermore, kinase domain is divided into two subdomains: a smaller N-terminal N-lobe and a larger C-terminal C-lobe. There is an ADP bounded to the cleft between N-lobe and C-lobe.

3
(Fig.3) Ire1 cytoplasm part

The dimer is bound together with some interactions which resident in two interfaces: N-lobe/N-lobe interface (Fig.4), and KEN domain/KEN domain interface (Fig.5). The amino acid residues forming these interactions are essential to the structure stability of Ire1. It was confirmed that Ire1 decreases significantly its functional ability by mutating these residues.

4 5
(Fig.4) N-lobe/N-lobe interface (Fig.5) KEN domain/KEN domain interface

A set of experiments conducted by Lee,K et al revealed that Ire1 dimerize through multi-processes. The dimerization mechanism of Ire1 proposed by them was described below. (Fig.6).

6
(Fig.6) The dimerization mechanism of Ire1

Step1:
Ire1 ER-luminal part dimerizes in response to the accumulation of misfolded protein.
This promoting the juxtaposition of two cytoplasmic kinase domains.

Step2:
The juxtaposition of two kinase domains promotes autophosphorylation of A-loop.
Then, phosphorylated A-loop permits nucleotide binding to kinase domain.

Step3:
ADP binding promotes dimerization of KEN domains.
This complete mode of dimer is fully competent for ribonuclease function.

The ribonuclease catalytic site of Ire1 is expected to be located near four residues(Y1049、R1056、N1057、H1061). (Fig.7). The arrangement of these four residues shows similarity to it of four ribonuclease catalytic residues in the tRNA-splicing endonuclease(xPSSS:2GJW). This fact indicates that the region is a candidate of the ribonuclease catalytic site. Further understanding of Ire1's ribonuclease catalytic mechanism awaits the crystal structure of Ire1 KEN domain in complex with RNA.

7 (Fig.7) The ribonuclease catalytic site of Ire1 KEN domain

Four residues remarked as yellow are expected to have direct relation of removing intron from the precursor mRNA.
The red dashed line represents B-loop which could not been determined by X-ray crystallographic analysis.

Protein Data Bank (PDB)

References

Source

Lee, K.P. Dey, M. Neculai, D. Cao, C. Dever, T.E. Sicheri, F.; "Structure of the dual enzyme ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing."; Cell(Cambridge,Mass.); (2008) 132:89-100 PubMed:18191223.

Others

author: Jun-ichi Ito


Japanese version:PDB:2RIO