(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Terrabacteria group: NE > Deinococcus-Thermus: NE > Deinococci: NE > Deinococcales: NE > Deinococcaceae: NE > Deinococcus: NE > Deinococcus radiodurans: NE
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 MNNSETPAPGPDSLLALAFPSDPQVSPDGKQVAFVLAQISEEDPAKPDKD FARPRYRSGLWLSEGGAARPLTHAETGRGDSAPRWSPDGQNLAFVRSAGE VKAALMLLPLKGGEARRVTHFKNGVSGPQWSPDGRFIAFTTTADTEDKRD ERGEARVLTRPVYRANGADWLPERPAALWLYDVEADKLREWYAPEIGIGA LSWWPDSRGVLIVQSEDEWQASQWRQDVYDLPLPTADAPAAPQKLLDWNS AAHGLAPHPDGQRFALIGRPAGKGNTEHAHLYLIENGQHRRLDTGHDHPV GDAVGGDCHVGAFPEGPRWLDGDTLLFSSTVRGSVGLFTAHIGGGVKAYD HDPQGVISAFTANEHGVALIRESATRFPEVELNGQRVTDLHARFPFPVRE PQRVTFETELGEGEGWVLLPEGEQKVPALLNIHGGPHTDYGHGFTHEFQL MAARGYGVCYSNPRGSVGYGQAWVDAIYGRWGTVDADDLLNFFDRCLEAV PRLDAAKTAVMGGSYGGFMTNWITGHTTRFQAAITDRCISNLISFGGTSD IGLRFWDDELGLDFSRRADALKLWDLSPLQYVENVKTPTLIVHSVLDHRC PVEQAEQWYAALHKHQVPVRFVRFPEENHELSRSGRPDRRLTRLNEYFAW LERWL
Serine peptidases of the prolyl oligopeptidase (POP) family are of substantial therapeutic importance because of their involvement in diseases such as diabetes, cancer, neurological diseases, and autoimmune disorders. Proper annotation and knowledge of substrate specificity mechanisms in this family are highly valuable. Although endopeptidase, dipeptidyl peptidase, tripeptidyl peptidase, and acylaminoacyl peptidase activities have been reported previously, here we report the first instance of carboxypeptidase activity in a POP family member. We determined the crystal structures of this carboxypeptidase, an S9C subfamily member from Deinococcus radiodurans, in its active and inactive states at 2.3-A resolution, providing an unprecedented view of assembly and disassembly of the active site mediated by an arginine residue. We observed that this residue is poised to bind substrate in the active structure and disrupts the catalytic triad in the inactive structure. The assembly of the active site is accompanied by the ordering of gating loops, which reduces the effective size of the oligomeric pore. This prevents the entry of larger peptides and constitutes a novel mechanism for substrate screening. Furthermore, we observed structural adaptations that enable its carboxypeptidase activity, with a unique loop and two arginine residues in the active site cavity orienting the peptide substrate for catalysis. Using these structural features, we identified homologs of this enzyme in the POP family and confirmed the presence of carboxypeptidase activity in one of them. In conclusion, we have identified a new type within POP enzymes that exhibits not only unique activity but also a novel substrate-screening mechanism.
Title: Expression, purification, crystallization and preliminary X-ray diffraction analysis of acylpeptide hydrolase from Deinococcus radiodurans Are VN, Ghosh B, Kumar A, Yadav P, Bhatnagar D, Jamdar SN, Makde RD Ref: Acta Crystallographica F Struct Biol Commun, 70:1292, 2014 : PubMed
Acylpeptide hydrolase (APH; EC 3.4.19.1), which belongs to the S9 family of serine peptidases (MEROPS), catalyzes the removal of an N-acylated amino acid from a blocked peptide. The role of this enzyme in mammalian cells has been suggested to be in the clearance of oxidatively damaged proteins as well as in the degradation of the beta-amyloid peptides implicated in Alzheimer's disease. Detailed structural information for the enzyme has been reported from two thermophilic archaea; both of the archaeal APHs share a similar monomeric structure. However, the mechanisms of substrate selectivity and active-site accessibility are totally different and are determined by inter-domain flexibility or the oligomeric structure. An APH homologue from a bacterium, Deinococcus radiodurans (APHdr), has been crystallized using microbatch-under-oil employing the random microseed matrix screening method. The protein crystallized in space group P21, with unit-cell parameters a = 77.6, b = 189.6, c = 120.4 A, beta = 108.4 degrees . A Matthews coefficient of 2.89 A(3) Da(-1) corresponds to four monomers, each with a molecular mass of approximately 73 kDa, in the asymmetric unit. The APHdr structure will reveal the mechanisms of substrate selectivity and active-site accessibility in the bacterial enzyme. It will also be helpful in elucidating the functional role of this enzyme in D. radiodurans.
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.
Deinococcus radiodurans acyl-peptide hydrolase, putative
