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PDBsum entry 4xzy
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PDB id:
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Hydrolase
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Title:
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Crystal structure of dipeptidyl peptidase 11 (dpp11) from porphyromonas gingivalis
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Structure:
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Peptidase s46. Chain: a, b. Engineered: yes
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Source:
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Porphyromonas gingivalis. Organism_taxid: 837. Gene: eg14_04230. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.70Å
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R-factor:
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0.185
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R-free:
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0.258
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Authors:
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Y.Sakamoto,Y.Suzuki,I.Iizuka,C.Tateoka,S.Roppongi,M.Fujimoto, T.Nonaka,W.Ogasawara,N.Tanaka
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Key ref:
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Y.Sakamoto
et al.
(2015).
Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Sci Rep,
5,
11151.
PubMed id:
DOI:
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Date:
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05-Feb-15
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Release date:
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15-Jul-15
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PROCHECK
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Headers
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References
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B2RID1
(DPP11_PORG3) -
Asp/Glu-specific dipeptidyl-peptidase from Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)
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Seq:
Struc:
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720 a.a.
699 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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DOI no:
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Sci Rep
5:11151
(2015)
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PubMed id:
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Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
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Y.Sakamoto,
Y.Suzuki,
I.Iizuka,
C.Tateoka,
S.Roppongi,
M.Fujimoto,
K.Inaka,
H.Tanaka,
M.Yamada,
K.Ohta,
H.Gouda,
T.Nonaka,
W.Ogasawara,
N.Tanaka.
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ABSTRACT
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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 biochemical studies revealed
that the side chain of Arg673 in the S1 subsite is essential for recognition of
the Asp/Glu side chain at the P1 position of the bound substrate. Because S46
peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we
anticipate that DPP11s could be utilised as targets for antibiotics. In
addition, the present structure analyses could be useful templates for the
design of specific inhibitors of DPP11s from pathogenic organisms.
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