(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Alphaproteobacteria: NE > Sphingomonadales: NE > Sphingomonadaceae: NE > Sphingobium: NE > Sphingobium faniae: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acide identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Sphingobium wenxiniae: N, E.
Molecular evidence
Database
No mutation 4 structures(e.g. : 5Y51, 5Y57, 5Y5R... more)(less) 5Y51: Crystal structure of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2 PytH_H230A, 5Y57: Crystal structure of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2, 5Y5R: Crystal structure of a novel Pyrethroid Hydrolase PytH with BIF, 5Y5V: Crystal structure of a novel Pyrethroid Hydrolase PytH (S78A) No kinetic
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MTVTDIILIHGALNRGACYDAVVPLLEARGYRVHAPDLTGHTPGDGGHLS VVDMEHYTRPVADILARAEGQSILLGHSLGGASISWLAQHHPDKVAGLIY LTAVLTAPGITPETFVLPGEPNRGTPHALDLIQPVDEGRGLQADFSRLER LREVFMGDYPGEGMPPAEQFIQTQSTVPFGTPNPMEGRALEIPRLYIEAL DDVVIPIAVQRQMQKEFPGPVAVVSLPASHAPYYSMPERLAEAIADFADA PAEYRQTATKAGPDRPAGADGGRADRADLP
References
Title: Structure and Catalytic Mechanism of a Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2 Xu D, Gao Y, Sun B, Ran T, Zeng L, He J, Wang W Ref: Applied Environmental Microbiology, :, 2020 : PubMed
Carboxylesterase PytH, isolated from a pyrethroid degrading bacterium Sphingobium faniae JZ-2, could rapidly hydrolyze the ester bond of a wide range of pyrethroid pesticides, including permethrin, fenpropathrin, cypermethrin, fenvalerate, deltamethrin, cyhalothrin and bifenthrin. To elucidate the catalytic mechanism of PytH, here we report the crystal structures of PytH with bifenthrin (BIF) and phenylmethylsulfonyl fluoride (PMSF) and two PytH mutants. Though PytH shares low sequence identity with reported alpha/beta-hydrolase fold proteins, the typical triad catalytic center with Ser-His-Asp triad (Ser78, His230 and Asp202) is present and vital for the hydrolase activity. However, no contact was found between Ser78 and His230 in the structures we solved, which may be due to the fact that the PytH structures we determined are in their inactive or low activity forms. The structure of PytH is composed of a core domain and a lid domain; some hydrophobic amino acid residues surrounding the substrate from both domains form a deeper and wider hydrophobic pocket than its homologous structures. This indicates that the larger hydrophobic pocket makes PytH fit for its larger substrates binding; both lid and core domains are involved in substrate binding and the lid domain induced core domain movement may make the active center correctly positioned with substrates.IMPORTANCE Pyrethroid pesticides are widely applied in agriculture and household, however, extensive use of these pesticides also causes serious environmental and health problems. The hydrolysis of pyrethroids by carboxylesterases is the major pathway of microbial degradation of pyrethroids, but the structure of carboxylesterases and its catalytic mechanism are still unknown. Carboxylesterase PytH from Sphingobium faniae JZ-2 could effectively hydrolyze a wide range of pyrethroid pesticides. The crystal structures of PytH are solved in this study. It showed that it belongs to the alpha/beta-hydrolase fold proteins with typical catalytic Ser-His-Asp triad though PytH has a low sequence identity (about 20%) with them. The special large hydrophobic binding pocket endowed PytH binding bigger pyrethroids family substrates. Our structures shed light on the substrate selectivity and the future application of PytH and deeper the understanding of alpha/beta-hydrolase members.
Title: Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product Wang BZ, Guo P, Hang BJ, Li L, He J, Li SP Ref: Applied Environmental Microbiology, 75:5496, 2009 : PubMed
A novel esterase gene, pytH, encoding a pyrethroid-hydrolyzing carboxylesterase was cloned from Sphingobium sp. strain JZ-1. The gene contained an open reading frame of 840 bp. Sequence identity searches revealed that the deduced enzyme shared the highest similarity with many alpha/beta-hydrolase fold proteins (20 to 24% identities). PytH was expressed in Escherichia coli BL21 and purified using Ni-nitrilotriacetic acid affinity chromatography. It was a monomeric structure with a molecular mass of approximately 31 kDa and a pI of 4.85. PytH was able to transform p-nitrophenyl esters of short-chain fatty acids and a wide range of pyrethroid pesticides, and isomer selectivity was not observed. No cofactors were required for enzyme activity.
Sphingobium faniae; Sphingobium wenxiniae, Pyrethroid hydrolase pytH
