(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 > Sphingomonas: NE > Sphingomonas sp. KT-1: NE
Molecular evidence
Database
No mutation 1 structure: 6VE6: A structural characterization of poly(aspartic acid) hydrolase-1 PahZ1 from Sphingomonas sp. KT-1. 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 MRPQKAAARALGLAVLVLAMTGGALGSPVTAGAAAAPAAASKGKAAALPD LKPGAGSFLFTGWAGKPLKVHYYAPDKITETTRILFVIHGAGRNADGYRD AWIPYAKEGQYIVLTPEYSMADFPTSLTYNVGHIVDEAGNPRPREEWSFA SIEPMFDQVRKATGSKVPTYAIYGHSAGGQFVHRFVELWPDARYSRAVAA NAGWYTMPDLAIKYPYGLKDAPTDAAGLKATLEKPLTILLGTADTDVNHH QLSRTPEAMTQGVHRLARGEFFYAYGRKVAHELNAKFAWKLDYAPDIAHS NTGMSQYAQKLVWE
Poly(aspartic acid) (PAA) is a green alternative to non-biodegradable poly(carboxylates) and has applications in both industrial and biomedical settings. PAA is synthesized by heating monomeric aspartic acid to yield a polysuccinamide that can be ring-opened to yield thermal PAA composed of 30% alpha-amide and 70% beta-amide linkages. Here, we report the first X-ray crystal structure of a PAA hydrolase from the bacteria Sphingomonas sp. KT-1 (PahZ1KT-1) which functions to degrade synthetic PAA to oligo(aspartic acid) by selective cleavage of beta-amide linkages. The structure was solved to 2.45 A and shows a dimeric assembly where each monomer maintains an alpha/beta hydrolase fold with a prominent, positively lined trough responsible for binding the anionic polymeric substrate. The putative catalytic sites of each monomer lie at the surface of the enzyme on opposite faces. The dimeric interface, as supported by small-angle X-ray scattering/multi-angle light scattering data, is primarily hydrophobic and is further stabilized by flanking hydrogen bonds. Molecular dynamics simulations support the previously determined specific cleavage of only the beta-amide linkage through a conformational change that aligns the substrate with the active site Ser. These data provide a scaffold for further understanding the mechanism of PAA hydrolysis and opens the opportunity for using protein engineering to catalyze the biodegradation of other xenobiotics.
Title: Genetic Analysis and Characterization of Poly(aspartic acid) Hydrolase-1 from Sphingomonas sp. KT-1 Hiraishi T, Kajiyama M, Tabata K, Yamato I, Doi Y Ref: Biomacromolecules, 4:80, 2003 : PubMed
Sphingomonas sp. KT-1 hydrolyzes poly(aspartic acid) (PAA) containing alpha- and beta-amide units and has at least two different types of PAA hydrolases. The PAA hydrolase-1 hydrolyzes selectively beta-beta amide units in PAA. Molecular cloning of PAA hydrolase-1 from Sphingomonas sp. KT-1 has been carried out to characterize its gene products. Genetic analysis shows that the deduced amino acid sequence of PAA hydrolase-1 has a similarity with those of the catalytic domain of poly(3-hydroxybutyric acid) (PHB) depolymerases from Alcaligenes faecalis AE122 and Pseudomonas lemoignei. Site-specific mutation analysis indicates that (176)Ser is a part of a strictly conserved pentapeptide sequence (Gly-Xaa-Ser-Xaa-Gly), which is the lipase box, and plays as an active residue.
Sphingomonas sp. KT-1. Poly(Aspartic acid) hydrolase-1
