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Information on EC 4.1.1.83 - 4-hydroxyphenylacetate decarboxylase and Organism(s) Clostridioides difficile and UniProt Accession Q84F16

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.83 4-hydroxyphenylacetate decarboxylase
IUBMB Comments
The enzyme, from the strict anaerobe Clostridium difficile, can also use (3,4-dihydroxyphenyl)acetate as a substrate, yielding 4-methylcatechol as a product. The enzyme is a glycyl radical enzyme.
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This record set is specific for:
Clostridioides difficile
UNIPROT: Q84F16
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The taxonomic range for the selected organisms is: Clostridioides difficile
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
4-hydroxyphenylacetate decarboxylase, 4hpad-ae, 4-hpd, p-hydroxyphenylacetate decarboxylase, 4hpad, p-hpd, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
p-hydroxyphenylacetate decarboxylase
-
4-hydroxyphenylacetate decarboxylase
-
-
HPA decarboxylase
-
-
p-hydroxyphenylacetate decarboxylase
pHPA decarboxylase
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
4-(hydroxyphenyl)acetate carboxy-lyase (4-methylphenol-forming)
The enzyme, from the strict anaerobe Clostridium difficile, can also use (3,4-dihydroxyphenyl)acetate as a substrate, yielding 4-methylcatechol as a product. The enzyme is a glycyl radical enzyme.
CAS REGISTRY NUMBER
COMMENTARY hide
340137-18-0
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(4-hydroxyphenyl)acetate + H+
4-methylphenol + CO2
show the reaction diagram
-
-
-
?
(3,4-dihydroxyphenyl)acetate + H+
4-methylcatechol + CO2
show the reaction diagram
-
-
-
-
?
(4-hydroxyphenyl)acetate + H+
4-methylphenol + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
indications for an as yet unidentified low molecular weight cofactor that is required for catalytic activity
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
-
28-32 iron atoms per native molecule
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(3,4-dihydroxyphenyl)acetate
-
-
4-hydroxymandelate
-
-
4-Hydroxyphenylacetamide
-
competitive
NaCl
-
800 mM, 50% inactivation
O2
-
readily and irreversibly inhibited
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.5
(3,4-dihydroxyphenyl)acetate
-
-
0.649 - 2.8
(4-hydroxyphenyl)acetate
0.41
3,4-Dihydroxyphenylacetate
-
in 100 mM Tris-HCl, pH 7.5, 40 mM NaCl, 5 mM MgCl2, 5 mM (NH4)2SO4, 5 mM cysteine, 25 mM substrate, and 5 mM dithiothreitol, at 30°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
110
(4-hydroxyphenyl)acetate
-
in 100 mM Tris-HCl, pH 7.5, 40 mM NaCl, 5 mM MgCl2, 5 mM (NH4)2SO4, 5 mM cysteine, 25 mM substrate, and 5 mM dithiothreitol, at 30°C
65
3,4-Dihydroxyphenylacetate
-
in 100 mM Tris-HCl, pH 7.5, 40 mM NaCl, 5 mM MgCl2, 5 mM (NH4)2SO4, 5 mM cysteine, 25 mM substrate, and 5 mM dithiothreitol, at 30°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
(3,4-dihydroxyphenyl)acetate
-
-
0.48
4-hydroxymandelate
-
-
0.7
4-Hydroxyphenylacetamide
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
HpdB protein
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
a truncated version of the activating protein devoid of the ferredoxin-like domain can activate the decarboxylase almost as fast as wild-type, but the generated glycyl radical is short living
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
HPDL_CLODI
902
0
101276
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
460000
hetero-octameric catalytically competent complex, gel filtration
105000
-
alpha,alpha‘, the smaller unit is a C-terminally truncated form, 1 * 110000 + 1 * 105000, SDS-PAGE
110000
-
alpha,alpha‘, the smaller unit is a C-terminally truncated form, 1 * 110000 + 1 * 105000, SDS-PAGE
200000
-
gel filtration
445000
-
SDS-PAGE
460000
hetero-octameric catalytically competent complex, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
beta2, decarboxylase purified from Clostridium difficile is an almost inactive homo-dimeric protein
octamer
beta4gamma4, small subunit HpdC has a molecular weight of 9598 Da as determined by MALDI TOF MS, the recombinant enzyme is a hetero-octameric catalytically competent complex
dimer
octamer
beta4gamma4, small subunit HpdC has a molecular weight of 9598 Da as determined by MALDI TOF MS, the recombinant enzyme is a hetero-octameric catalytically competent complex
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
phosphorylation of the small subunit is responsible for th change in oligomeric state from inactive homo-dimeric protein of Clostridium difficile to the recombinant hetero-octameric catalytically competent complex
phosphoprotein
phosphorylation of the small subunit is responsible for th change in oligomeric state from inactive homo-dimeric protein of Clostridium difficile to the recombinant hetero-octameric catalytically competent complex
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
0°C in presence of 1 mM sodium sulfide and 5 mM ammonium sulfate
658599
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
half-life: 15 min, in presence of 1 mM sodium sulfide and 5 mM ammonium sulfate
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
readily and irreversibly inhibited by O2
-
658599
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, 100 mM Tris/HCl, pH 7.5, 5 mM ammonium sulfate, 1 mM magnesium chloride, more than 90% of the activity is recovered after 5 days
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Streptactin-Macroprep column chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloning of three genes encoding two subunits of the glycyl-radical enzyme and the activating enzyme, expressed in Escherichia coli
cloning of three genes encoding two subunits of the glycyl-radical enzyme and the activating enzyme, expressed in Escherichia coli
expressed in Escherichia coli Rosetta (DE3) pLysS cells
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
D'Ari, L.; Barker, H.A.
p-Cresol formation by cell-free extracts of Clostridium difficile
Arch. Microbiol.
143
311-312
1985
Clostridioides difficile
Manually annotated by BRENDA team
Selmer, T.; Andrei, P.I.
p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol
Eur. J. Biochem.
268
1363-1372
2001
Clostridioides difficile
Manually annotated by BRENDA team
Andrei, P.I.; Pierik, A.J.; Zauner, S.; Andrei-Selmer, L.C.; Selmer, T.
Subunit composition of the glycyl radical enzyme p-hydroxyphenylacetate decarboxylase. A small subunit, HpdC, is essential for catalytic activity
Eur. J. Biochem.
271
2225-2230
2004
Clostridioides difficile (Q84F14), Clostridioides difficile (Q84F15), Clostridioides difficile (Q84F16), Clostridioides difficile
Manually annotated by BRENDA team
Yu, L.; Blaser, M.; Andrei, P.I.; Pierik, A.J.; Selmer, T.
4-hydroxyphenylacetate decarboxylases: Properties of a novel subclass of glycyl radical enzyme systems
Biochemistry
45
9584-9592
2006
Clostridioides difficile, Clostridium scatologenes, Clostridium scatologenes 957
Manually annotated by BRENDA team
Selvaraj, B.; Pierik, A.J.; Bill, E.; Martins, B.M.
The ferredoxin-like domain of the activating enzyme is required for generating a lasting glycyl radical in 4-hydroxyphenylacetate decarboxylase
J. Biol. Inorg. Chem.
19
1317-1326
2014
Clostridioides difficile
Manually annotated by BRENDA team