9CR6

Crystal structure of histidine racemase (HisR) of Fusobacterium nucleatum (C209S)

9CR6 の概要

• エントリーDOI: 10.2210/pdb9cr6/pdb
• 関連するPDBエントリー: 9CR1
• 分子名称: Histidine racemase, PHOSPHATE ION (3 entities in total)
• 機能のキーワード: d-histidine, racemase, stereochemistry, cofactor-independent, lanthionine, fusobacterium nucleatum, staphylopine, cntk, staphylococcus aureus, isomerase
• 由来する生物種: Fusobacterium nucleatum
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 124634.78

構造登録者

Chen, P.,Lamer, T.,Vederas, J.C.,Lemieux, M.J. (登録日: 2024-07-20, 公開日: 2025-03-05)

主引用文献

Lamer, T.,Chen, P.,Venter, M.J.,van Belkum, M.J.,Wijewardane, A.,Wu, C.,Lemieux, M.J.,Vederas, J.C.
Discovery, characterization, and structure of a cofactor-independent histidine racemase from the oral pathogen Fusobacterium nucleatum.
J.Biol.Chem., 300:107896-107896, 2024

PubMed Abstract: Fusobacterium nucleatum is an oral commensal bacterium that can act as an opportunistic pathogen and is implicated in diseases such as periodontitis, adverse pregnancy outcomes, colorectal cancer, and Alzheimer's disease. F. nucleatum synthesizes lanthionine for its peptidoglycan, rather than meso-2,6-diaminopimelic acid (DAP) used by most Gram-negative bacteria. Despite lacking the biosynthetic pathway for DAP, the genome of F. nucleatum ATCC 25586 encodes a predicted DAP epimerase. A recent study hypothesized that this enzyme may act as a lanthionine epimerase, but the authors found a very low turnover rate, suggesting that this enzyme likely has another more favored substrate. Here, we characterize this enzyme as a histidine racemase (HisR), and found that catalytic turnover is ∼10,000× faster with L-histidine than with L,L-lanthionine. Kinetic experiments suggest that HisR functions as a cofactor-independent racemase and that turnover is specific for histidine, while crystal structures of catalytic cysteine to serine mutants (C67S or C209S) reveal this enzyme in its substrate-unbound, open conformation. Currently, the only other reported cofactor-independent histidine racemase is CntK from Staphylococcus aureus, which is used in the biosynthesis of staphylopine, a broad-spectrum metallophore that increases virulence of S. aureus. However, CntK shares only 28% sequence identity with HisR, and their genes exist in different genomic contexts. Knockout of hisR in F. nucleatum results in a small but reproducible lag in growth compared to WT during exponential phase, suggesting that HisR may play a role in growth of this periodontal pathogen.

PubMed: 39424140
DOI: 10.1016/j.jbc.2024.107896

実験手法

X-RAY DIFFRACTION (2.49 Å)