9IZ4
Crystal structure of phosphonopyruvate decarboxylase RhiEF from Bacillus subtilis ATCC6633 in complex with thiamine pyrophosphate
Summary for 9IZ4
| Entry DOI | 10.2210/pdb9iz4/pdb |
| Related | 9IZ3 |
| Descriptor | Putative phosphonopyruvate decarboxylase alpha subunit, Putative phosphonopyruvate decarboxylase beta subunit, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | phosphonopyruvate decarboxylase, rhief, rhizocticin biosynthesis, thiamine pyrophosphate, lyase |
| Biological source | Bacillus spizizenii ATCC 6633 = JCM 2499 More |
| Total number of polymer chains | 12 |
| Total formula weight | 248660.35 |
| Authors | Nakamura, A.,Kojima, S. (deposition date: 2024-07-31, release date: 2024-12-18, Last modification date: 2025-01-01) |
| Primary citation | Nakamura, A.,Shiina, A.,Fukaya, T.,Seki, Y.,Momiyama, M.,Kojima, S. Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase. Biochemistry, 63:3250-3260, 2024 Cited by PubMed Abstract: The RhiE and RhiF proteins work together as RhiEF and function as a thiamine pyrophosphate (TPP)-dependent phosphonopyruvate decarboxylase to produce phosphonoacetaldehyde in the rhizocticin biosynthesis pathway. In this study, we determined the crystal structure of the RhiEF complexed with TPP and Mg. RhiEF forms a dimer of heterodimers, and the cofactor TPP is bound at the heterotetrameric subunit interface. Structural analysis of RhiEF revealed that the RhiE and RhiF moieties correspond to the pyrimidine-binding (PYR) and pyrophosphate-binding (PP) domains commonly found in TPP-dependent enzymes, respectively, as predicted by amino acid sequence alignment analysis. In contrast to other TPP-dependent enzymes with known structures, RhiEF has no domains other than the PYR and PP domains. Furthermore, structure-based evolutionary and sequence-based phylogenetic analyses have suggested that heteromultimeric enzymes such as RhiEF are ancestral types. These results indicate that RhiEF is one of the smallest and most ancient TPP-dependent decarboxylases. Based on the structural comparisons of RhiEF with other TPP-dependent decarboxylases, we identified the amino acid residues responsible for the catalytic mechanism of TPP-dependent decarboxylation in RhiEF. PubMed: 39586109DOI: 10.1021/acs.biochem.4c00559 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.05 Å) |
Structure validation
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