4RHE

Crystal structure of UbiX, an aromatic acid decarboxylase from the Colwellia psychrerythraea 34H

Summary for 4RHE

• Entry DOI: 10.2210/pdb4rhe/pdb
• Related: 4RHF
• Descriptor: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase, FLAVIN MONONUCLEOTIDE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rossmann fold, decarboxylase, lyase
• Biological source: Colwellia psychrerythraea 34H
• Total number of polymer chains: 6
• Total formula weight: 140440.42

Authors

Do, H.,Kim, S.J.,Lee, C.W.,Kim, H.-W.,Park, H.H.,Kim, H.M.,Park, H.,Park, H.J.,Lee, J.H. (deposition date: 2014-10-02, release date: 2015-02-18, Last modification date: 2024-02-28)

Primary citation

Do, H.,Kim, S.J.,Lee, C.W.,Kim, H.W.,Park, H.H.,Kim, H.M.,Park, H.,Park, H.,Lee, J.H.
Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes.
Sci Rep, 5:8196-8196, 2015

PubMed Abstract: The ubiX gene of Colwellia psychrerythraea strain 34H encodes a 3-octaprenyl-4-hydroxybenzoate carboxylase (CpsUbiX, UniProtKB code: Q489U8) that is involved in the third step of the ubiquinone biosynthesis pathway and harbors a flavin mononucleotide (FMN) as a potential cofactor. Here, we report the crystal structures of two forms of CpsUbiX: an FMN-bound wild type form and an FMN-unbound V47S mutant form. CpsUbiX is a dodecameric enzyme, and each monomer possesses a typical Rossmann-fold structure. The FMN-binding domain of UbiX is composed of three neighboring subunits. The highly conserved Gly15, Ser41, Val47, and Tyr171 residues play important roles in FMN binding. Structural comparison of the FMN-bound wild type form with the FMN-free form reveals a significant conformational difference in the C-terminal loop region (comprising residues 170-176 and 195-206). Subsequent computational modeling and liposome binding assay both suggest that the conformational flexibility observed in the C-terminal loops plays an important role in substrate and lipid bindings. The crystal structures presented in this work provide structural framework and insights into the catalytic mechanism of CpsUbiX.

PubMed: 25645665
DOI: 10.1038/srep08196

Experimental method

X-RAY DIFFRACTION (2.003 Å)