9U3C

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with L-Proline

Summary for 9U3C

• Entry DOI: 10.2210/pdb9u3c/pdb
• Descriptor: Monomeric sarcosine oxidase, FLAVIN-ADENINE DINUCLEOTIDE, PROLINE, ... (8 entities in total)
• Functional Keywords: sarcosine oxidase, oxidoreductase
• Biological source: Bacillus sp. B-0618
• Total number of polymer chains: 2
• Total formula weight: 91090.90

Authors

Zhang, Y.,Nakajima, Y.,Kurobe, M.,Nakamura, T.,Himiyama, T.,Nishiya, Y. (deposition date: 2025-03-18, release date: 2025-09-24)

Primary citation

Zhang, Y.,Nakajima, Y.,Kurobe, M.,Nakamura, T.,Himiyama, T.,Nishiya, Y.
Structural and functional analysis of Bacillus sarcosine oxidase and its activity toward cyclic imino acids.
Febs Open Bio, 2025

PubMed Abstract: This study investigated the reactivity of sarcosine oxidase (Sox) toward minor substrates through kinetic and structural analyses, along with mutational engineering to elucidate their reaction mechanisms. Sarcosine oxidase from Bacillus sp. (SoxB) recognizes the cyclic imino acids l-proline (l-Pro), d-proline (d-Pro), and l-thioproline (l-Tpr) as minor substrates. The reaction behavior varied depending on the substrates; notably, the absorption spectrum of l-Tpr exhibited charge transfer, which was characteristic of substrate inhibition. Crystal structures of the enzyme-substrate complexes suggested that Tyr254 causes spatial interference with cyclic imino acids at the active site. The Tyr254Ala and Tyr254Gly mutants exhibited enhanced reactivity toward cyclic imino acids by eliminating this spatial interference. Crystallographic analysis of the mutants revealed an enlarged active site, which facilitated reactions with five-membered cyclic imino acids. These mutations disrupted the electron delocalization associated with l-Tpr, thereby eliminating charge transfer and substrate inhibition. A water network was also identified near the enzyme's active site, interacting with the side chain of Tyr254. These findings provide valuable insights into substrate specificity and may facilitate the development of enzymes with broader substrate scope and enhanced catalytic activity.

PubMed: 40932061
DOI: 10.1002/2211-5463.70119

Experimental method

X-RAY DIFFRACTION (1.54 Å)