Any feedback?
Information on EC 4.1.1.19 - arginine decarboxylase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q57764
for references in articles please use BRENDA:EC4.1.1.19Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
4.1.1.19 arginine decarboxylaseIUBMB Comments
A pyridoxal-phosphate protein.
Specify your search results
Word Map
- 4.1.1.19
- polyamine
- putrescine
- ornithine
- spermidine
- s-adenosylmethionine
- arginase
-
diamine
- samdc
- decarboxylases
- agmatinase
- deiminase
- alpha-difluoromethylornithine
- cadaverine
-
imidazoline
- d-arginine
- pao
-
3.5.3.1
-
iminohydrolase
-
arginine-dependent
-
scots
-
ureohydrolase
- difluoromethylornithine
-
pyrogenic
- drug development
- agriculture
- hyoscyamine
- trifoliata
- poncirus
- speb
-
tropane
- dl-alpha-difluoromethylornithine
- antizyme
- datura
The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
arginine decarboxylase, spea2, argdc, spea1, biosynthetic arginine decarboxylase, ppadc, pyruvoyl-dependent arginine decarboxylase, atadc2, l-arginine decarboxylase, ptadc, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ADC
-
-
-
-
ARGDC
-
-
-
-
bADC
-
-
-
-
Biosynthetic arginine decarboxylase
-
-
-
-
dADC
-
-
-
-
Decarboxylase, arginine
-
-
-
-
L-Arginine decarboxylase
-
-
-
-
Synthetic arginine decarboxylase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
L-arginine carboxy-lyase (agmatine-forming)
A pyridoxal-phosphate protein.
CAS REGISTRY NUMBER
COMMENTARY
9024-77-5
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-arginine
agmatine + CO2
enzyme catalyzes the first step of the polyamine-biosynthetic pathway
-
-
?
L-arginine
agmatine + CO2
-
enzyme is involved in polyamine biosynthesis
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-arginine
agmatine + CO2
enzyme catalyzes the first step of the polyamine-biosynthetic pathway
-
-
?
L-arginine
agmatine + CO2
-
enzyme is involved in polyamine biosynthesis
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
the pyruvoyl group of the enzyme is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains
-
additional information
-
the pyruvoyl group of the enzyme is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains
-
additional information
the enzyme contains a reactive pyruvoyl group, the proenzyme undergoes autocatalytic serinolysis, resulting in the formation of two chains and the creation of a pyruvoyl group, which is the cofactor for the decarboxylation reaction
-
additional information
-
the enzyme contains a reactive pyruvoyl group, the proenzyme undergoes autocatalytic serinolysis, resulting in the formation of two chains and the creation of a pyruvoyl group, which is the cofactor for the decarboxylation reaction
-
additional information
-
the enzyme contains a reactive pyruvoyl group
-
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.002
murtant N47A, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine
0.132
mutant E109Q, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine
1.014
wild type enzyme, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 8
-
pH 5.0: about 60% of maximal activity, pH 8.0: about 60% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
trimer
trimer
Mutant E109Q, the structure contains 2 complete trimers in the asymmetric unit, the active sites of each trimer are located between adjacent protomers. All 6 protomers are fully processed and contain the product agmatine at the active site. The presence of the product agmatine confirms that the mutant is active because the substrate arginine is added to the protein during crystallization.
trimer
Mutant N47A, the structure contains 2 complete trimers in the asymmetric unit, the active sites of each trimer are located between adjacent protomers. The mutant protein does not show complete processing in all protomers. The first protomer of N47A is processed showing clear cleavage of the protomer to form the beta-chain (residues 1-52) and the alpha-chain (residues 53-165). A second protomer is unprocessed, showing clear density connecting residues Ser52 and Ser53. The final protomer in the first trimer can not easily be classified as either processed or unprocessed and is likely to be a mixture of the two states. The density between Ser52 and Ser53 is weak, density is also present corresponding to the pyruvoyl group and the product agmatine.
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
the pyruvoyl group of the enzyme is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction
proteolytic modification
-
the enzyme is formed by self-cleavage of a proenzyme into a 5000 Da subunit and a 12000 Da subunit that contains a reactive pyruvoyl group
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of enzyme labeled with selenomethionine, enzyme-agmatine complex and S53A mutant structure, hanging drop method, determination of structure at 1.4 A, crystals belong to space group P2, with cell dimensions a = 56.77 A, b = 92.99 A, c = 87.23 A, and beta = 94.84°
the N47A and E109Q mutant proteins are co-crystallized at 22°C with 1-2 mM arginine, the hanging-drop vapor-diffusion method is used. Crystals are grown in 17-20% PEG 2000, 10% 2-methyl-2,4-pentanediol, 2.5% glycerol, 100 mM HEPES pH 6.7-7.3, 0.5 mM beta-octylglucoside, 0.5 mM ethylenediaminetetraacetic acid and 10 mM dithiothreitol.
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E109Q
E109Q mutation reduces the activity by 7.7fold compared to the wild type enzyme, reduced decarboxylation activity results in part from incomplete pyruvoyl-group formation
N47A
The activity of N47A is reduced by 500fold compared with the wild type protein
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme resists proteolytic cleavage by trypsin, pepsin, carboxypeptidase A, or papain
-
enzyme retains full activity in presence of 1% w/v SDS at 70°C
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purification and cleavage of the N-terminal His-tag are performed
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
Escherichia coli strain MachI is used as a recipient for transformations during plasmid construction and for plasmid propagation and storage. Site-directed mutagenesis is performed on pPRDC.19. The mutant plasmids are transformed into Escherichia coli B834 (DE3) competent cells.
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Graham, D.E.; Xu, H.; White, R.H.
Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis
J. Biol. Chem.
277
23500-23507
2002
Methanocaldococcus jannaschii
Tolbert, W.D.; Graham, D.E.; White, R.H.; Ealick, S.E.
Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms
Structure
11
285-294
2003
Methanocaldococcus jannaschii (Q57764), Methanocaldococcus jannaschii
Soriano, E.V.; McCloskey, D.E.; Kinsland, C.; Pegg, A.E.; Ealick, S.E.
Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii
Acta Crystallogr. Sect. D
64
377-382
2008
Methanocaldococcus jannaschii (Q57764), Methanocaldococcus jannaschii
EXTERNAL LINKS (specific for EC-Number 4.1.1.19)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
