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7BRA

Bacillus subtilis IRG1

Summary for 7BRA
Entry DOI10.2210/pdb7bra/pdb
DescriptorBacillus subtilis IRG1, 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, SULFATE ION, ... (4 entities in total)
Functional Keywordsirg1, cis-aconitate decarboxylase, immune-responsive gene 1 protein, structural protein
Biological sourceBacillus subtilis
Total number of polymer chains2
Total formula weight96336.92
Authors
Park, H.H.,Chun, H.L. (deposition date: 2020-03-27, release date: 2021-02-03, Last modification date: 2023-11-29)
Primary citationChun, H.L.,Lee, S.Y.,Lee, S.H.,Lee, C.S.,Park, H.H.
Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis.
Sci Rep, 10:11305-11305, 2020
Cited by
PubMed Abstract: Itaconate, which is formed by decarboxylation of cis-aconitate-an intermediate metabolite in the tricarboxylic acid cycle-has been used as a building block in polymer synthesis and is an important chemical in several biomedical and industrial applications. Itaconate is an immunometabolite with antibacterial, antiviral, immunoregulatory, and tumor-promoting activities. Recent focus has been on the role of itaconate in the field of immunology, with immune-responsive gene 1 (IRG1) being identified as the cis-aconitate decarboxylase responsible for itaconate production. We solved the structure of IRG1 from Bacillus subtilis (bsIRG1) and showed that IRG1 adopts either a closed or an open conformation; bsIRG1 was in the open form. A1 and A2 loops around the active site are flexible and can control the formation of the open and closed forms of IRG1. An in silico docking simulation showed that only the open form of IRG1 can accommodate the substrate. The most energetically favorable position of cis-aconitate in the active site of bsIRG1 involved the localization of C2 and C5 of cis-aconitate into the H102 region and H151 region of bsIRG1, respectively. Based on the structural study of bsIRG1, compared with IDS epimerase, and in silico docking simulation, we proposed two tentative enzymatic reaction mechanisms of IRG1, a two-base model and a one-base model.
PubMed: 32647315
DOI: 10.1038/s41598-020-68419-y
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.785 Å)
Structure validation

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