6JQX

Crystal structure of a hydrogenase from Trichosporon moniliiforme

Summary for 6JQX

• Entry DOI: 10.2210/pdb6jqx/pdb
• Descriptor: Salicylate decarboxylase, 2-HYDROXYBENZOIC ACID, ZINC ION, ... (4 entities in total)
• Functional Keywords: structure function, salicylate, decarboxylase, hydrolase
• Biological source: Cutaneotrichosporon moniliiforme (Yeast)
• Total number of polymer chains: 2
• Total formula weight: 80721.35

Authors

Qin, H.M.,Chen, X.T. (deposition date: 2019-04-01, release date: 2020-04-01, Last modification date: 2023-11-22)

Primary citation

Gao, X.,Wu, M.,Zhang, W.,Li, C.,Guo, R.T.,Dai, Y.,Liu, W.,Mao, S.,Lu, F.,Qin, H.M.
Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel.
J.Agric.Food Chem., 69:11616-11625, 2021

PubMed Abstract: Salicylic acid (SA) decarboxylase from (TmSdc), which reversibly catalyses the decarboxylation of SA to yield phenol, is of significant interest because of its potential for the production of benzoic acid derivatives under environmentally friendly reaction conditions. TmSdc showed a preference for C2 hydroxybenzoate derivatives, with / of SA being 3.2 × 10 M s. Here, we presented the first crystal structures of TmSdc, including a complex with SA. The three conserved residues of Glu8, His169, and Asp298 are the catalytic residues within the TIM-barrel domain of TmSdc. Trp239 forms a unique hydrophobic recognition site by interacting with the phenyl ring of SA, while Arg235 is responsible for recognizing the hydroxyl group at the C2 of SA via hydrogen bond interactions. Using a semi-rational combinatorial active-site saturation test, we obtained the TmSdc mutant MT3 (Y64T/P191G/F195V/E302D), which exhibited a 26.4-fold increase in / with SA, reaching 8.4 × 10 M s. Steered molecular dynamics simulations suggested that the structural changes in MT3 relieved the steric hindrance within the substrate access channel and enlarged the substrate-binding pocket, leading to the increased activity by improving substrate access. Our data elucidate the unique substrate recognition mode and the substrate entrance tunnel of SA decarboxylase.

PubMed: 34553918
DOI: 10.1021/acs.jafc.1c04091

Experimental method

X-RAY DIFFRACTION (1.672 Å)