9iz4 | pdb_00009iz4

Crystal structure of phosphonopyruvate decarboxylase RhiEF from Bacillus subtilis ATCC6633 in complex with thiamine pyrophosphate

spinqualitylabelsall models 9iz4, resolution 3.05Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9iz4 is a 12 chain structure with sequence from Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.05Å Ligands: MG, SPV, TPP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D4HRI2_BACSC Publication Abstract from PubMed 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(2+). 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. Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase.,Nakamura A, Shiina A, Fukaya T, Seki Y, Momiyama M, Kojima S Biochemistry. 2024 Dec 17;63(24):3250-3260. doi: 10.1021/acs.biochem.4c00559. , Epub 2024 Nov 25. PMID:39586109 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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