2015
DOI: 10.1038/srep11151
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Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity

Abstract: The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and bioche… Show more

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Cited by 14 publications
(32 citation statements)
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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%
“…). 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%
“…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%
See 1 more Smart Citation
“…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%