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Information on EC 3.5.1.B15 - pyrazinamidase and Organism(s) Mycobacterium tuberculosis and UniProt Accession I6XD65

for references in articles please use BRENDA:EC3.5.1.B15
preliminary BRENDA-supplied EC number
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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.1 In linear amides
                3.5.1.B15 pyrazinamidase
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Mycobacterium tuberculosis
UNIPROT: I6XD65 not found.
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The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The expected taxonomic range for this enzyme is: Archaea, Bacteria
Synonyms
pyrazinamidase, pyrazinamidase/nicotinamidase, bspnca, more
SYSTEMATIC NAME
IUBMB Comments
pyrazinamide amidohydrolase
-
CAS REGISTRY NUMBER
COMMENTARY hide
39419-71-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
nicotinamide + H2O
nicotinate + NH3
show the reaction diagram
-
-
-
?
pyrazinamide + H2O
pyrazinoic acid + NH3
show the reaction diagram
pyrazinamide + H2O
pyrazinoic acid + NH3
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
nicotinamide + H2O
nicotinate + NH3
show the reaction diagram
-
-
-
?
pyrazinamide + H2O
pyrazinoic acid + NH3
show the reaction diagram
pyrazinamide + H2O
pyrazinoic acid + NH3
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
activates, and reactivates the metal-depleted PZase
Ni2+
activates, and facilitates the deprotonation of coordinates water molecules to generate a nucleophile that catalyzes the enzymatic reaction
Fe2+
-
the iron binding site residues are Asp49, His51, His57, and His71
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
glycerol
increases the enzyme activity up to 130% at 37°C, gives rise to an increase in the content of alpha-helix and beta-sheets elements. More stability of PZase in glycerol solution correlates with its amphiphilic orientation, which decreases the unfavorable interactions of hydrophobic regions.
sorbitol
increases the enzyme activity up to 110% at 37°C, gives rise to an increase in the content of alpha-helix and beta-sheets elements
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.431 - 0.79
Pyrazinamide
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.725 - 2
Pyrazinamide
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.68 - 2.53
Pyrazinamide
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
computational insights into pH-dependence of structure and dynamics of pyrazinamidase, comparison of wild-type and mutant enzymes
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
pyrazinamide (PZA), a derivative of nicotinamide is one of the most imperative first-line drug treatments against tuberculosis. PZA is significantly used in MDR tuberculosis in combination with isoniazid, rifampicin and ethambutol in regimens. The most potent action of the drug is against the semi-dormant bacilli in an acidic environment, which cannot be treated with most other drugs and thus helps in shortening the chemotherapy period
physiological function
malfunction
physiological function
pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid, by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase)
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39700
dimeric enzyme, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 20500-20700, about, recombinant enzyme, SDS-PAGE and mass spectrometry. Homodimers show a slightly lower specific enzyme activity compared to monomers. Enzyme dimers are dissociated into monomers in response to reducing conditions, disulfide bonds C72-C138 and C138-C138 stabilize the quaternary structure of the enzyme homodimer, quarternary structure analysis, structural model of enzyme homodimer, overview
monomer
1 * 20500-20700, about, recombinant enzyme, SDS-PAGE and mass spectrometry. Homodimers show a slightly lower specific enzyme activity compared to monomers. Enzyme dimers are dissociated into monomers in response to reducing conditions, disulfide bonds C72-C138 and C138-C138 stabilize the quaternary structure of the enzyme homodimer, quarternary structure analysis, overview
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
analysis of enzyme crystal structure, PDB ID 3PL1
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A146V
naturally occuring mutation, the mutant shows 72% reduced activity compared to wild-type, resistant strain
C138Y
site-directed mutagenesis
D126N
site-directed mutagenesis, the mutation causes pyrazinamide resistance, the mutation is located outside of active site and has an allosteric affect
D136G
site-directed mutagenesis, the mutation highly reduces the mutant activity compared to wild-type
D63A
naturally occuring mutation, susceptible strain
E144K
naturally occuring mutation from PZA-resistant isolate, analysis of the resistance mechanism of the mutant strain
F94L
site-directed mutagenesis
G24D
site-directed mutagenesis
G97D
naturally occuring mutation, the mutant shows 90% reduced activity compared to wild-type, resistant strain
H51P
naturally occuring mutation, inactive mutant, resistant strain
H51Q
site-directed mutagenesis
I5T
naturally occuring mutation, the mutant shows 88% reduced activity compared to wild-type, resistant strain
I6L
naturally occuring mutation, susceptible strain
K96R
naturally occurring mutation in the PncA catalytic region, binding cavity analysis shows an increase of 762.3 A3 in the volume of the mutant protein. Docking studies reveal that pyrazinamide (PZA) has a greater binding affinity for the wild-type protein in comparison to the mutant protein. The residues of flap region acquire more flexibility in mutant form of protein and thus move away from the active site. This leads to weak binding of the drug to the target residues. The mutation leads to a substantial increase in the binding cavity. This prohibits the enzyme from holding the drug properly and therefore pyrazinoic acid (PZA) cannot take its active form
L116P
site-directed mutagenesis
L19R
naturally occuring mutation from PZA-resistant isolate
L85P
naturally occuring mutation, resistant strain
L85R
naturally occuring mutation, inactive mutant, resistant strain
M175V
naturally occuring mutation, susceptible strain
N11K
site-directed mutagenesis, the active site mutation causes pyrazinamide resistance, destabilization of the Fe2+ binding site
P62T
naturally occuring mutation, susceptible strain
P69T
site-directed mutagenesis, the active site mutation causes pyrazinamide resistance, destabilization of the Fe2+ binding site
P77L/V131G
naturally occuring mutation, susceptible strain
R140H
naturally occuring mutation from PZA-resistant isolate
R140S
naturally occuring mutation, susceptible strain
S67P
site-directed mutagenesis
T135P
T142R
T167I
naturally occuring mutation, susceptible strain
T47A
naturally occuring mutation, susceptible strain
T47P
naturally occuring mutation, inactive mutant, resistant strain
T87M
site-directed mutagenesis, active mutant, susceptible strain
T92C
the naturally occuring mutation causes an increase in distance from metal ion position to enzyme active site, but it is considered as a polymorphism
V155G
naturally occuring mutation, resistant strain
V7A
naturally occuring mutation, susceptible strain
V9A
naturally occuring mutation, the mutant shows 73% reduced activity compared to wild-type, resistant strain
V9G
naturally occuring mutation, the mutant shows 99% reduced activity compared to wild-type, resistant strain
W68G
naturally occuring mutation, resistant strain
Y64D
naturally occuring mutation, susceptible strain
Y99S
naturally occuring mutation, susceptible strain
A143T
-
site-directed mutagenesis, the mutation decreases the Km and kcat values of the enzyme
A143T/T168A/E173K
-
site-directed mutagenesis, the mutation decreases the Km and kcat values of the enzyme, the mutant shows reduced thermostability compared to wild-type
L151S
-
site-directed mutagenesis, the mutant has a weakened binding affinity for pyrazinamide and reduced thermostability compared to the wild-type
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis in alcohols, i.e. methanol, ethanol, isopropanol and n-propanol, are analyzed in the presence of absence of stabilizing osmolytes, sorbitol, sucrose and glycerol, overview. Methanol destabilizes, while glacerol stabilizes the enzyme. A decrease in the tertiary structure of the enzyme is less in the presence of ethanol, compared to the solutions of other alcohols. These results indicate that methanol, isopropanol and n-propanol decrease the tertiary structure of PZase in a similar manner
kinetics of activation and half-life of wild-type and mutant PZases
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Methanol
can interact with PZase via hydrophobic interactions and hydrogen bonds resulting in destabilization of the structure of the enzyme. Glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography, ultrafiltration, and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and ultrafiltration
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene pncA, DNA and amino acid sequence determination and analysis of enzyme mutants, genotyping
gene pncA, DNA and amino acid sequence determination and analysis, recombinant enzyme expression in Escherichia coli strain BL21(DE3)pLysS
gene pncA, genotyping, DNA and amino acid sequence determination and analysis of wild-type and mutants
gene pncA, PCR-based in vitro expression, and recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain TOP10
gene pncA, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
recombinant overexpression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 (DE3)
gene pncA, genotyping, global statistics for 641 mutations in 171 (of 187) codons from 2760 resistant strains and 96 mutations from 3329 susceptible strains reported in 61 studies, overview
-
gene pncA, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain DH5alpha
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
diagnostics
-
the pyrazinamidase activity in pyrazinamide (PZA)-resistant isolates is an important parameter to determine the susceptibility to pyrazinoic acid (PZA) because PZase converts PZA into pyrazinoic acid, which is protonated and becomes active against the mycobacterium. A nonfunctional PZase allows the mycobacterium to survive in the presence of PZA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Rueda, D.; Sheen, P.; Gilman, R.H.; Bueno, C.; Santos, M.; Pando-Robles, V.; Batista, C.V.; Zimic, M.
Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds
Tuberculosis
94
644-648
2014
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Ramirez-Busby, S.M.; Valafar, F.
Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates
Antimicrob. Agents Chemother.
59
5267-5277
2015
Mycobacterium tuberculosis
Manually annotated by BRENDA team
Vats, C.; Dhanjal, J.; Goyal, S.; Gupta, A.; Bharadvaja, N.; Grover, A.
Mechanistic analysis elucidating the relationship between Lys96 mutation in Mycobacterium tuberculosis pyrazinamidase enzyme and pyrazinamide susceptibility
BMC Genomics
16(Suppl 2)
S14
2015
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Rasool, N.; Husssain, W.; Khan, Y.D.
Revelation of enzyme activity of mutant pyrazinamidases from Mycobacterium tuberculosis upon binding with various metals using quantum mechanical approach
Comput. Biol. Chem.
83
107108
2019
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Pazhang, M.; Mardi, N.; Mehrnejad, F.; Chaparzadeh, N.
The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds
Int. J. Biol. Macromol.
108
1339-1347
2018
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Khajehzadeh, M.; Mehrnejad, F.; Pazhang, M.; Doustdar, F.
Effects of sorbitol and glycerol on the structure, dynamics, and stability of Mycobacterium tuberculosis pyrazinamidase
Int. J. Mycobacteriol.
5 Suppl 1
S138-S139
2016
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Rueda, D.; Bernard, C.; Gandy, L.; Capton, E.; Boudjelloul, R.; Brossier, F.; Veziris, N.; Zimic, M.; Sougakoff, W.
Estimation of pyrazinamidase activity using a cell-free in vitro synthesis of pnca and its association with pyrazinamide susceptibility in Mycobacterium tuberculosis
Int. J. Mycobacteriol.
7
16-25
2018
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65), Mycobacterium tuberculosis variant bovis
Manually annotated by BRENDA team
Khan, M.T.; Malik, S.I.
Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance
J. Biomol. Struct. Dyn.
38
3003-3017
2020
Mycobacterium tuberculosis (A0A2Z5CVM9), Mycobacterium tuberculosis
Manually annotated by BRENDA team
Esmaeeli, R.; Mehrnejad, F.; Mir-Derikvand, M.; Gopalpoor, N.
Computational insights into pH-dependence of structure and dynamics of pyrazinamidase A comparison of wild type and mutants
J. Cell. Biochem.
120
2502-2514
2018
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Khan, M.; Junaid, M.; Mao, X.; Wang, Y.; Hussain, A.; Malik, S.; Wei, D.
Pyrazinamide resistance and mutations L19R, R140H, and E144K in pyrazinamidase of Mycobacterium tuberculosis
J. Cell. Biochem.
120
7154-7166
2019
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Junaid, M.; Khan, M.T.; Malik, S.I.; Wei, D.Q.
Insights into the mechanisms of the pyrazinamide resistance of three pyrazinamidase mutants N11K, P69T, and D126N
J. Chem. Inf. Model.
59
498-508
2019
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Aono, A.; Chikamatsu, K.; Yamada, H.; Igarashi, Y.; Murase, Y.; Takaki, A.; Mitarai, S.
A simplified pyrazinamidase test for pyrazinamide drug susceptibility in Mycobacterium tuberculosis
J. Microbiol. Methods
154
52-54
2018
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Khadem-Maaref, M.; Mehrnejad, F.; Phirouznia, A.
Effects of metal-ion replacement on pyrazinamidase activity a quantum mechanical study
J. Mol. Graph. Model.
73
24-29
2017
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Rasool, N.; Iftikhar, S.; Amir, A.; Hussain, W.
Structural and quantum mechanical computations to elucidate the altered binding mechanism of metal and drug with pyrazinamidase from Mycobacterium tuberculosis due to mutagenicity
J. Mol. Graph. Model.
80
126-131
2018
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team
Doustdar, F.; Pazhang, M.; Mehrnejad, F.; Safarzadeh, M.; Rabiei, D.; Chaparzadeh, N.; Falahati, H.; Mir-Derikvand, M.
Biochemical characterization and computational identification of Mycobacterium tuberculosis pyrazinamidase in some pyrazinamide-resistant isolates of Iran
Protein J.
34
181-192
2015
Mycobacterium tuberculosis
Manually annotated by BRENDA team
Ahmadi, A.; Nazari, R.; Arjomandzadegan, M.; Zolfaghari, M.R.; Vahidi, V.; Poolad, T.; Kahbazi, M.; Sadrnia, M.; Tousheh, M.; Rafiee, P.
Insights into pyrazinamidase and DNA gyrase protein structures in resistant and susceptible clinical isolates of Mycobacterium tuberculosis
Tanaffos
15
147-153
2016
Mycobacterium tuberculosis (I6XD65), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (I6XD65), Mycobacterium tuberculosis H37Rv (I6XD65)
Manually annotated by BRENDA team