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Information on EC 3.4.19.1 - acylaminoacyl-peptidase and Organism(s) Aeropyrum pernix and UniProt Accession Q9YBQ2

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EC Tree
     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.19 Omega peptidases
                3.4.19.1 acylaminoacyl-peptidase
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This record set is specific for:
Aeropyrum pernix
UNIPROT: Q9YBQ2 not found.
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Word Map
The taxonomic range for the selected organisms is: Aeropyrum pernix
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide
Synonyms
apaap, acylpeptide hydrolase, acylaminoacyl peptidase, acylamino acid-releasing enzyme, acyl-peptide hydrolase, spaap, aphdr, acyl peptide hydrolase, apaph, aare/oph, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acyl-peptide hydrolase
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acylamino-acid-releasing enzyme
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acylaminoacyl peptidase
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Acylaminoacyl-peptidase
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acylpeptide hydrolase
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acylpeptide hydrolase/esterase
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alpha-N-acylpeptide hydrolase
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DNF15S2 protein
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N-acylaminoacyl-peptide hydrolase
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N-acylpeptide hydrolase
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N-formylmethionine (fMet) aminopeptidase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide
show the reaction diagram
substrate binding and catalytic mechanisms, overview. Three main pathways are observed most frequently, namely P1, P2A, and P3, evaluation by comparing the average force profiles and potential of mean force calculations revealing that P3 is the unbinding pathway. P1 is located in a tunnel in the beta-propeller domain and contained the D158, R160, S157, S201, A200, S199, W250, D69, Q28, and R287 residues. P2A is located between blades 1 and 2 (G86, E88, K85, H90, D82, and N65), whereas P2D penetrates through blades 1 and 2 formed by loop A, which is close to P2A (S481, F485, D482, L115, I114, R113, H90, E88, R526, and S525). P3 is located between the beta-propeller domain and alpha/beta hydrolase containing the residues M561, A564, L568, F381, T380, I20, A21, F41, K24, G40, G44, and V46
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of peptide bond
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PATHWAY SOURCE
PATHWAYS
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CAS REGISTRY NUMBER
COMMENTARY hide
73562-30-8
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala + H2O
2-aminobenzoyl-Ala-Leu-Phe + Gln-Gly-Pro-Phe(NO2)-Ala
show the reaction diagram
endopeptidase activity
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?
4-nitrophenyl caprylate + H2O
4-nitrophenol + caprylate
show the reaction diagram
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?
Ac-Ala-Ala + H2O
Ac-Ala + Ala
show the reaction diagram
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?
Ac-Ala-Ala-Ala + H2O
Ac-Ala + Ala-Ala
show the reaction diagram
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?
Ac-Ala-Ala-Ala-Ala + H2O
Ac-Ala + Ala-Ala-Ala
show the reaction diagram
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?
Ac-Leu-4-nitroanilide + H2O
Ac-Leu + 4-nitroaniline
show the reaction diagram
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?
acetyl-Phe-2-naphthylamide + H2O
acetyl-Phe + 2-naphthylamine
show the reaction diagram
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?
N-acetyl-L-Leu-4-nitroanilide + H2O
N-acetyl-L-Leu + 4-nitroaniline
show the reaction diagram
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?
N-acetyl-Leu-4-nitroanilide + H2O
N-acetyl-L-Leu + 4-nitroaniline
show the reaction diagram
switch of substrate specificity of hyperthermophilic promiscuous acylaminoacyl peptidase by combination of protein and solvent engineering into a specific carboxylesterase
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?
N-acetyl-Leu-p-nitroanilide + H2O
N-acetyl-Leu + p-nitroaniline
show the reaction diagram
esterase activity of wild-type enzyme with p-nitrophenyl caprylate as substrate is 7times higher than peptidase activity with N-acetyl-Leu-p-nitroanilide as substrate, 150fold higher for mutant enzyme R526V, peptidase activity for mutant R526E is abolished
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?
N-acetyl-Phe-2-naphthylamide + H2O
N-acetyl-Phe + 2-naphthylamine
show the reaction diagram
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p-nitrophenyl caprylate + H2O
nitrophenol + caprylate
show the reaction diagram
esterase activity of wild-type enzyme with p-nitrophenyl caprylate as substrate is 7times higher than peptidase activity with N-acetyl-Leu-p-nitroanilide as substrate, 150fold higher for mutant enzyme R526V, peptidase activity for mutant R526E is abolished
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?
additional information
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Acetyl-Phe
forms hydrogen bonds with both NH groups of the oxyanion binding site of AAP. In the mutant enzyme the NH bond of Gly369 points in a different direction
benzyloxycarbonyl-Gly-Gly-Phe-chloromethyl ketone
CMK, chloromethyl ketone inhibitor, enzyme binding structure analysis, molecular dynamics studies, overview
chlorpyrifos
binding structure, docking study, and molecular dynamics simulations using structure PDB ID 1VE7 as search model, and umbrella sampling calculations, molecular mechanical/GBSA calculations, enzyme-inhibitor complex structure, overview
chlorpyrifosmethyl oxon
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additional information
different organophosphorous compounds bind to the enzyme inducing conformational changes in two domains, namely, alpha/beta hydrolase and beta-propeller, computational study of APH bound to chlorpyrifosmethyl oxon and dichlorvos, and molecular dynamics simulations of enzyme bound to the inhibitors, the starting model of APH is derived from 2.7 A resolution crystal structure of acylpeptide hydrolase/esterase from Aeropyrum pernix K1 (PDB ID 1VE7), overview. The docking study reveals that Val471 and Gly368 are important residues for chlorpyrifosmethyl oxon and dichlorvos binding
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00129 - 0.0071
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
0.0082 - 0.1
acetyl-Phe-2-naphthylamide
0.4 - 10.5
N-acetyl-Leu-p-nitroanilide
0.00566
N-acetyl-Phe-2-naphthylamide
pH 7.0, 70°C, wild-type enzyme
35.7 - 114.6
p-nitrophenyl caprylate
additional information
additional information
thermodynamics
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000917 - 8.2
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
0.5 - 26.9
N-acetyl-Leu-p-nitroanilide
4.28
N-acetyl-Phe-2-naphthylamide
pH 7.0, 70°C, wild-type enzyme
6.6 - 30.9
p-nitrophenyl caprylate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.129 - 6347
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
0.414 - 865
N-acetyl-Phe-2-naphthylamide
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0105 - 0.0178
Acetyl-Phe
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
wild-type enzyme
8.8
wild-type enzyme
9
the rate constants for the D524A and D524N variants increase to about pH 9
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8 - 8.8
pH 5.8: about% of maximal activity, pH 8.8: about% of maximal activity
7.5 - 9.5
pH 7.5: about 50% of maximal activity, pH 9.5: about 65% of maximal activity, wild-type enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
wild-type enzyme
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60 - 80
60°C: about 40% of maximal activity, 80°C: optimum
additional information
the enzyme is thermophilic
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
physiological function
acylpeptide hydrolases (APHs) catalyze the removal of N-acylated amino acids from blocked peptides
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
symmetric homodimer with each subunit comprised of two domains. The N-terminal domain is a regular seven-propeller, while the C-terminal domain has a canonical alpha/beta hydrolase fold and includes the active site and a conserved Ser445-Asp524-His556 catalytic triad
homodimer
the monomer subunit is composed of one hydrolase and one propeller domain. In the homodimeric structures only one subunit displayed the closed form of the enzyme. The other subunit exhibits an open gate to the catalytic site, thus revealing the structural basis that controls the oligopeptidase activity
additional information
APH family is composed of a beta-propeller domain in N-terminus and a catalytic domain in C-terminus. These domains are structurally connected by bridge regions. One is the N-terminus region that stretches into the C-terminal catalytic domain. The other is the linker that directly connects the beta-propeller domain to the catalytic domain. N-terminus region forms a unique alpha-helix 1 (alpha1), which deviates from the beta-propeller domain. Nevertheless, it connects with the surface of the catalytic domain. The structure of alpha1 is conserved and affects conformational flexibility
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals grown at 17.8°C using ammonium phosphate as a precipitant. Crystals belong to space group P1 with unit-cell parameters a = 107.5, b = 109.9, alpha = 108.1°, beta = 109.8° and gamma = 91.9°
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crystals of the H367A mutant grown at 20°C in hanging drops, to 2.2 A resolution. Belongs to space group P212121
hanging drop method, crystal structure determination of the native and two mutant structures (D524N and D524A)
hanging-drop vapor-diffusion method. The best crystals were obtained from reservoir of 6% PEG4000, 50 mM/l NaAc (pH 4.6), 15 mM/l DTT, 0.2 mM/l EDTA
purified enzyme in complex with chloromethyl ketone inhibitor, hanging drop vapour diffusion method, for the complex crystal form: mixing of 0.003 ml of protein solution containing 0.221 mM ApAAP protein, and 0.56 mM inhibitor CMK in 20 mM Tris pH 7.5 buffer, with 0.003 ml of reservoir solution containing 78 mM sodium acetate, pH 4.5, 2.4% w/v PEG 4000, 6.7 mM dithiothreitol, and 0.44 mM EDTA, for apoenzyme crystal form: mixing of 0.003 ml of protein solution containing 0.158 mM ApAAP protein in 20 mM Tris pH 7.5 buffer, with 0.003 ml of reservoir solution containing 78 mM sodium acetate, pH 5.0, 2.2% w/v PEG 4000, 5.2 mM dithiothreitol, and 0.34 mM EDTA, 20°C, X-ray diffraction structure determination and analysis at 1.90A and 2.55A resolution, modeling
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D524A
the mutation affects the closed, active form of the enzyme, disrupting its catalytic triad. The wild-type enzyme exhibits a bell-shaped pH-rate profile (optimum at pH 7.5), whereas the rate constants for the D524A and D524N variants increase to about pH 9. The kcat/Km values is much lower compared with those of the wild-type enzyme
D524N
the mutation affects the closed, active form of the enzyme, disrupting its catalytic triad. The wild-type enzyme exhibits a bell-shaped pH-rate profile (optimum at pH 7.5), whereas the rate constants for the D524A and D524N variants increase to about pH 9. The kcat/Km values is much lower compared with those of the wild-type enzyme
F488G/R526V/T560W
1.55fold increase in activity with 4-nitrophenyl laurate compared to activity of mutant R526V/T560W
H367A
displays significantly reduced catalytic activity. Unlike the reaction of the wild-type, the reaction of the mutant displays completely linear temperature dependence. Its reaction is associated with unfavourable entropy of activation
R526 I
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 17.3fold higher than the wild-type ratio
R526A
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 11.7fold higher than the wild-type ratio
R526E
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 115.5fold higher than the wild-type ratio
R526K
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 13.9fold higher than the wild-type ratio
R526L
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 14.8fold higher than the wild-type ratio
R526V
R526V/T560W
1.5fold increase in activity with 4-nitrophenyl dodecanoate compared to activity of mutant R526V
W474V/F488G/R526V/T560W
the mutant enzyme has 7fold higher catalytic efficiency (kcat/Km) for 4-nitrophenyl dodecanoate than the mutant enzyme R526V
W474V/R526V/T560W
3.11fold increase in activity with 4-nitrophenyl laurate compared to activity of mutant R526V/T560W
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
both the wild-type and the H367A mutant are stable up to 90°C but tend to denature at higher temperature, more readily with the mutant. At lower temperature the wild-type has more flexible structural elements, particularly at 25°C, but differences diminish with increase of temperature
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli of of chimeras of a carboxylesterase (EC 3.1.1.1) from Archaeoglobus fulgidus and an acylpeptide hydrolase (EC 3.4.19.1) from Aeropyrum pernix K1
gene APE_1547.1, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
enzyme APH is believed to be an important target for drug design
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, G.; Gao, R.; Ding, Y.; Yang, H.; Cao, S.; Feng, Y.; Rao, Z.
Crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix
Acta Crystallogr. Sect. D
58
1054-1055
2002
Aeropyrum pernix
Manually annotated by BRENDA team
Wang, Q.; Yang, G.; Liu, Y.; Feng, Y.
Discrimination of esterase and peptidase activities of acylaminoacyl peptidase from hyperthermophilic Aeropyrum pernix K1 by a single mutation
J. Biol. Chem.
281
18618-18625
2006
Aeropyrum pernix (Q9YBQ2)
Manually annotated by BRENDA team
Bartlam, M.; Wang, G.; Yang, H.; Gao, R.; Zhao, X.; Xie, G.; Cao, S.; Feng, Y.; Rao, Z.
Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
Structure
12
1481-1488
2004
Aeropyrum pernix (Q9YBQ2)
Manually annotated by BRENDA team
Kiss, A.L.; Pallo, A.; Naray-Szabo, G.; Harmat, V.; Polgar, L.
Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase
J. Struct. Biol.
162
312-323
2008
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix K1 (Q9YBQ2)
Manually annotated by BRENDA team
Zhou, X.; Wang, H.; Zhang, Y.; Gao, L.; Feng, Y.
Alteration of substrate specificities of thermophilic alpha/beta hydrolases through domain swapping and domain interface optimization
Acta Biochim. Biophys. Sin.
44
965-973
2012
Aeropyrum pernix (Q9YBQ2)
Manually annotated by BRENDA team
Harmat, V.; Domokos, K.; Menyhard, D.K.; Pallo, A.; Szeltner, Z.; Szamosi, I.; Beke-Somfai, T.; Naray-Szabo, G., Polgar, L.
Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase
J. Biol. Chem.
286
1987-1998
2011
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix DSM 11879 (Q9YBQ2)
Manually annotated by BRENDA team
Papaleo, E.; Renzetti, G.
Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal alpha-helix in an acylaminoacyl peptidase
J. Mol. Graph. Model.
38
226-234
2012
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2)
Manually annotated by BRENDA team
Liu, C.; Yang, G.; Wu, L.; Tian, G.; Zhang, Z.; Feng, Y.
Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering
Protein Cell
2
497-506
2011
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2)
Manually annotated by BRENDA team
Menyhard, D.K.; Orgovan, Z.; Szeltner, Z.; Szamosi, I.; Harmat, V.
Catalytically distinct states captured in a crystal lattice the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality
Acta Crystallogr. Sect. D
71
461-472
2015
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2)
Manually annotated by BRENDA team
Liu, D.; Deng, L.; Wang, D.; Li, W.; Gao, R.
"Bridge regions" regulate catalysis and protein stability of acylpeptide hydrolase
Biochem. Eng. J.
145
42-52
2019
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2), Sulfurisphaera tokodaii (Q973W9), Sulfurisphaera tokodaii 7 (Q973W9), Sulfurisphaera tokodaii DSM 16993 (Q973W9), Sulfurisphaera tokodaii JCM 10545 (Q973W9), Sulfurisphaera tokodaii NBRC 100140 (Q973W9)
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Manually annotated by BRENDA team
Jin, H.; Zhou, Z.; Wang, D.; Guan, S.; Han, W.
Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos
Int. J. Mol. Sci.
16
6217-6234
2015
Aeropyrum pernix (Q9YBQ2)
Manually annotated by BRENDA team
Wang, D.; Jin, H.; Wang, J.; Guan, S.; Zhang, Z.; Han, W.
Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations
J. Biomol. Struct. Dyn.
34
749-761
2016
Aeropyrum pernix (Q9YBQ2)
Manually annotated by BRENDA team
Zhu, J.; Wang, Y.; Li, X.; Han, W.; Zhao, L.
Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations
J. Biomol. Struct. Dyn.
36
4285-4302
2018
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2), Homo sapiens (P13798), Homo sapiens
Manually annotated by BRENDA team
Jin, H.; Zhu, J.; Dong, Y.; Han, W.
Exploring the different ligand escape pathways in acylaminoacyl peptidase by random acceleration and steered molecular dynamics simulations
RSC Adv.
6
10987-10996
2016
Aeropyrum pernix (Q9YBQ2)
-
Manually annotated by BRENDA team