Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity

Sakamoto, Yasumitsu; Suzuki, Yoshiyuki; Iizuka, I.; Tateoka, C.; Roppongi, S.; Fujimoto, Masashi; Inaka, Koji; Tanaka, Hiroaki; Yamada, Michihiro; Ohta, Kazunori; Gouda, Hiroaki; Nonaka, Takamasa; Ogasawara, Wataru; Tanaka, Nobutada

doi:10.1038/srep11151

Cited by 14 publications

(32 citation statements)

References 56 publications

(94 reference statements)

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“…). Similarly, in crystal structure of S46 family peptidase (DPP‐11, dipeptidyl peptidase 11) (PDB code, 4Y01) that is specific toward substrates with N‐terminal Asp/Glu, a cluster of Arg residues was observed in the vicinity of the S1 subsite . Hence, in the serine peptidases that are specific for N‐terminal acidic residue, the Arg residues of active site pocket seem to be important for providing the suitable electrostatic potential for substrate binding.…”

Section: Resultsmentioning

confidence: 98%

Structure of Asp‐bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition

et al. 2018

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Peptidase-E, a nonclassical serine peptidase, is specific for dipeptides with an N-terminal aspartate. This stringent substrate specificity remains largely unexplained. We report an aspartate-bound structure of peptidase-E at 1.83 Å resolution. In contrast to previous reports, the enzyme forms a dimer, and the active site is located at the dimer interface, well shielded from the solvent. Our findings further suggest that the stringent aspartate specificity of the enzyme is due to electrostatics and molecular complementarity in the active site. The new structural information presented herein may provide insights into the role of functionally important residues in peptidase-E.

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Section: Resultsmentioning

confidence: 98%

Structure of Asp‐bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition

et al. 2018

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“…Ser 691 (PgDPP11 numbering) [21,22]. Among the ten residues, Gly 652 , Arg 673 , Gly 677 , Gly 680 , and…”

Section: Bfdpp11 3d Structural Modeling and Mechanism Of Its Inefficimentioning

confidence: 99%

“…The role of Arg 337 of PgDPP11 has been extensively examined [21] and its substitution to Asn, Ala, and Gly was shown to lead to a significant increase in enzymatic activity. Thus, the Arg337Asn substitution of BfDPP11 could not explain the activity reduction of BfDPP11.…”

Section: Bfdpp11 3d Structural Modeling and Mechanism Of Its Inefficimentioning

confidence: 99%

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Identification of a new subtype of dipeptidyl peptidase 11 and a third group of the S46-family members specifically present in the genus Bacteroides

et al. 2018

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Peptidase family S46 consists of two types of dipeptidyl-peptidases (DPPs), DPP7 and DPP11, which liberate dipeptides from the N-termini of polypeptides along with the penultimate hydrophobic and acidic residues, respectively. Their specificities are primarily defined by a single amino acid residue, Gly in DPP7 and Arg in DPP11 (numbering for Porphyromonas gingivalis DPP11). Bacterial species in the phyla Proteobacteria and Bacteroidetes generally possess one gene for each, while Bacteroides species exceptionally possess three genes, one gene as DPP7 and two genes as DPP11, annotated based on the full-length similarities. In the present study, we aimed to characterize the above-mentioned Bacteroides S46 DPPs. A recombinant protein of the putative DPP11 gene BF9343_2924 from Bacteroides fragilis harboring Gly exhibited DPP7 activity by hydrolyzing Leu-Leu-4-methylcoumaryl-7-amide (MCA). Another gene, BF9343_2925, as well as the Bacteroides vulgatus gene (BVU_2252) with Arg was confirmed to encode DPP11. These results demonstrated that classification of S46 peptidase is enforceable by the S1 essential residues. Bacteroides DPP11 showed a decreased level of activity towards the substrates, especially with P1-position Glu. Findings of 3D structural modeling indicated three potential amino acid substitutions responsible for the reduction, one of which, Asn650Thr substitution, actually recovered the hydrolyzing activity of Leu-Glu-MCA. On the other hand, the gene currently annotated as DPP7 carrying Gly from B. fragilis (BF9343_0130) and Bacteroides ovatus (Bovatus_03382) did not hydrolyze any of the examined substrates. The existence of a phylogenic branch of these putative Bacteroides DPP7 genes classified by the C-terminal conserved region (Ser-Leu) strongly suggests that Bacteroides species expresses a DPP with an unknown property. In conclusion, the genus Bacteroides exceptionally expresses three S46-family members; authentic DPP7, a new subtype of DPP11 with substantially reduced specificity for Glu, and a third group of S46 family members.

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“…Recently, crystal structures of PgDPP11 were solved 27,28 , and those of Porphyromonas endodontalis DPP11 (PeDPP11) have also been reported 28 . PgDPP11 is a homodimer, and each subunit contains a peptidase domain, including a double β-barrel fold that is characteristic of the chymotrypsin superfamily 29,30 , as well as an unusual α-helical domain that regulates the exopeptidase activity of PgDPP11.…”

Section: Introductionmentioning

confidence: 99%

Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase

Sakamoto

Suzuki

Watanabe

et al. 2019

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Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.

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Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity

Cited by 14 publications

References 56 publications

Structure of Asp‐bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition

Structure of Asp‐bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition

Identification of a new subtype of dipeptidyl peptidase 11 and a third group of the S46-family members specifically present in the genus Bacteroides

Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase

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