PDBsum entry 2be1

Transcription

PDB id: 2be1

Contents

Protein chains

301 a.a. *

Ligands

VAL-VAL-VAL-VAL-VAL-VAL-VAL-VAL

Waters ×26

* Residue conservation analysis

PDB id:

2be1

Name:

Transcription

Title:

Structure of the compact lumenal domain of yeast ire1

Structure:

Serine/threonine-protein kinase/endoribonuclease ire1. Chain: a, b. Fragment: residues 111-449, lumenal domain. Synonym: endoplasmic reticulum-to-nucleus signaling 1. Engineered: yes. Peptide. Chain: d. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ire1, ern1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: co-crystallized peptide of unknown origin and sequence

Biol. unit:

Trimer (from PQS)

Resolution:

2.98Å R-factor: 0.244 R-free: 0.279

Authors:

J.J.Credle,J.S.Finer-Moore,F.R.Papa,R.M.Stroud,P.Walter

Key ref:

J.J.Credle et al. (2005). On the mechanism of sensing unfolded protein in the endoplasmic reticulum. Proc Natl Acad Sci U S A, 102, 18773-18784. PubMed id: 16365312 DOI: 10.1073/pnas.0509487102

Date:

21-Oct-05 Release date: 13-Dec-05

Protein chains

P32361  (IRE1_YEAST) -  Serine/threonine-protein kinase/endoribonuclease IRE1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1115 a.a.

Struc: 301 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 3: E.C.3.1.26.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0509487102

Proc Natl Acad Sci U S A 102:18773-18784 (2005)

PubMed id: 16365312

On the mechanism of sensing unfolded protein in the endoplasmic reticulum.

J.J.Credle, J.S.Finer-Moore, F.R.Papa, R.M.Stroud, P.Walter.

ABSTRACT

Unfolded proteins in the endoplasmic reticulum (ER) activate the ER transmembrane sensor Ire1 to trigger the unfolded protein response (UPR), a homeostatic signaling pathway that adjusts ER protein folding capacity according to need. Ire1 is a bifunctional enzyme, containing cytoplasmic kinase and RNase domains whose roles in signal transduction downstream of Ire1 are understood in some detail. By contrast, the question of how its ER-luminal domain (LD) senses unfolded proteins has remained an enigma. The 3.0-A crystal structure and consequent structure-guided functional analyses of the conserved core region of the LD (cLD) leads us to a proposal for the mechanism of response. cLD exhibits a unique protein fold and is sufficient to control Ire1 activation by unfolded proteins. Dimerization of cLD monomers across a large interface creates a shared central groove formed by alpha-helices that are situated on a beta-sheet floor. This groove is reminiscent of the peptide binding domains of major histocompatibility complexes (MHCs) in its gross architecture. Conserved amino acid side chains in Ire1 that face into the groove are shown to be important for UPR activation in that their mutation reduces the response. Mutational analyses suggest that further interaction between cLD dimers is required to form higher-order oligomers necessary for UPR activation. We propose that cLD directly binds unfolded proteins, which changes the quaternary association of the monomers in the membrane plane. The changes in the ER lumen in turn position Ire1 kinase domains in the cytoplasm optimally for autophosphorylation to initiate the UPR.

Selected figure(s)

Figure 1.
Fig. 1. The Ire1 cLD. (A) The relative conservation of amino acids is plotted along the sequence of Ire1 LD. The blue bar represents the cLD, the structure of which is shown below. The gray bars represent regions that were disordered in LD crystals and absent in cLD crystals. The black bar represents the signal sequence (ss). (B) Amino acid alignment of IRE1 and PERK LDs. (S.c., Saccharomyces cerevisiae; K.l., Kluveromyces lactis; C.e., Caenorhabditis elegans; D.m., Drosophila melanogaster; M.m., Muscus musculus-a; I, Ire1 cLD; P, PERK cLD. Conservation of residues among species was scored by using BLOSSUM62 (46). Blue represents residues of high conservation. Secondary structural elements are indicated above the alignment and correspond in color to those of the ribbon diagram of the Ire1 cLD in C. Dashed lines (L1 and L2) represent regions found disordered in the structure. The asterisks mark residues that have been mutated in this study. For each sequence, amino acid number 1 is the initiating Met. The D.m. sequence is incorrect in the databases; an in-house resequenced sequence is used in the alignment (Julie Hollien and Jonathan Weissman, personal communication). The PERK sequence has two additional insertions (amino acids 286-314 and 413-428) where indicated. (C) Ribbon diagram of the cLD dimer as seen in the asymmetric unit corresponding to residues 111-449 have been colored with a rainbow gradient with from N terminus (blue) to C terminus (red). (D) Schematic connectivity diagram (road map) of the cLD using the same coloring scheme as in B and C.

Figure 5.
Fig. 5. Model for unfolded protein recognition by Ire1. The model depicts Ire1 activation through oligomerization brought about by binding of unfolded proteins (indicated in red). Direct or indirect interactions between unfolded protein chains may contribute to activation. On the ER-luminal side of the membrane, the postulated unfolded protein-binding groove formed by Ire1 cLD dimerization through Interface 1 is indicated in dark gray. On the cytoplasmic side of the ER membrane, oligomerization juxtaposes the Ire1 kinase domains, which undergo a conformational change after autophosphorylation that activates the RNase function of Ire1. Inactive Ire1 could either be monomeric as shown or exist already in oligomeric yet inactive states whose quaternary associations change upon unfolded protein binding.

Figures were selected by the author.