Information on EC 5.4.3.4 - D-lysine 5,6-aminomutase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
5.4.3.4
-
RECOMMENDED NAME
GeneOntology No.
D-lysine 5,6-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
radical catalytic mechanism
-
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
catalytic mechanism, overview
-
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
radical stabilization is crucial in the mechanism of action of lysine 5,6-aminomutase, role of Tyr263alpha. The enzyme utilizes free radical intermediates to mediate 1,2-amino group rearrangement, during which an elusive high-energy aziridincarbinyl radical is proposed to be central in the mechanism of action. The aziridincarbinyl radical acts either as a spin-relay device or serves as an anchor for the pyridine ring of pyridoxal-5' -phosphate through aromatic PI-stacking interactions during spin transfer, detailed overview
-
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
-
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
Clostridium sticklandii StadtmanHF, Propionibacterium freudenreichii ATCC 9614
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
group transfer
-
-
intramolecular, amino group
-
isomerization
-
-
-
-
isomerization
-
-
PATHWAY
KEGG Link
MetaCyc Link
Lysine degradation
-
SYSTEMATIC NAME
IUBMB Comments
D-2,6-diaminohexanoate 5,6-aminomutase
Requires a cobamide coenzyme.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5,6-LAM
Clostridium sticklandii StadtmanHF
-
-
-
5,6-LAM
Propionibacterium freudenreichii ATCC 9614
-
-
-
alpha-Lysine mutase
-
-
-
-
Aminomutase, D-lysine 5,6-
-
-
-
-
D-alpha-lysine mutase
-
-
-
-
lysine 5,6-aminomutase
Clostridium sticklandii StadtmanHF
-
-
-
lysine 5,6-aminomutase
-
-
lysine 5,6-aminomutase
-
-
lysine 5,6-aminomutase
Propionibacterium freudenreichii ATCC 9614
-
-
-
mutase, D-alpha-lysine
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9075-70-1
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
Clostridium sticklandii StadtmanHF
-
-
-
Manually annotated by BRENDA team
Propionibacterium freudenreichii ATCC 9614
subsp. shermanii
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
evolution
-
the enzyme belongs to the class III dAdoCbl-dependent isomerase family
metabolism
-
lysine 5,6-aminomutase participates in the fermentation of L- or D-lysine as carbon and nitrogen sources in anaerobic bacteria
metabolism
-
the enzyme participates in the second step of the fermentation pathway of lysine in which lysine is converted to acetic acid, ammonia and butyric acid
additional information
-
active site structure, overview. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. The recombinant enzyme (KamDE) containing only E1 is active, but is subjected to suicide inactivation with the substrate. Modeling of the closed conformation of the enzyme, domain motions, overview
additional information
-
a large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. The recombinant enzyme (KamDE) containing only E1 is active, but is subjected to suicide inactivation with the substrate
additional information
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
additional information
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal-5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
additional information
Clostridium sticklandii StadtmanHF
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
-
additional information
Propionibacterium freudenreichii ATCC 9614
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal-5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
-
-, 5,6-LAM has both beta-lysine 5,6-aminomutase and D-lysine 5,6-aminomutase activity
-
?
4-thia-D-lysine
?
show the reaction diagram
-
substrate analogue, suicide inhibitor
-
-
?
4-thia-L-lysine
?
show the reaction diagram
-
substrate analogue, suicide inhibitor
-
-
?
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
D-alpha-Lysine
?
show the reaction diagram
[Clostridium] sticklandii
-
enzyme of lysine fermentation pathway
-
-
-
D-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
equilibrium constant of 1.2
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii StadtmanHF, Propionibacterium freudenreichii ATCC 9614
-
-
-
-
r
D-lysine
D-2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
L-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-, first step in D-lysine catabolism
-
r
L-lysine
L-2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
additional information
?
-
[Clostridium] sticklandii
-
5-fluorolysine as substrate binding in the active site: computational simulations, the enzyme 5,6-LAM abstracts the hydrogen atom rather than the fluorine at C5 of 5-fluorolysine and subsequent rearrangement mimicking the similar mechanism as the natural substrate of the enzyme
-
-
-
additional information
?
-
[Clostridium] sticklandii
-
the enzyme can accept D-lysine and L-beta-lysine
-
-
-
additional information
?
-
-
the enzyme can accept D-lysine and L-beta-lysine
-
-
-
additional information
?
-
[Clostridium] sticklandii, Porphyromonas gingivalis
-
the enzyme can accept D-lysine and L-beta-lysine. The enzyme employs radical generating capability of coenzyme B12, i.e. 5'-deoxyadenosylcobalamin, and ability of pyridoxal 5'-phosphate, i.e. vitamin B6, to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons
-
-
-
additional information
?
-
[Clostridium] sticklandii StadtmanHF, Propionibacterium freudenreichii ATCC 9614
-
the enzyme can accept D-lysine and L-beta-lysine
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
-
-
-
?
D-alpha-Lysine
?
show the reaction diagram
[Clostridium] sticklandii
-
enzyme of lysine fermentation pathway
-
-
-
D-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
r
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
equilibrium constant of 1.2
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii StadtmanHF, Propionibacterium freudenreichii ATCC 9614
-
-
-
-
r
L-lysine
2,5-diaminohexanoate
show the reaction diagram
[Clostridium] sticklandii
-
first step in D-lysine catabolism
-
r
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
-
-
5'-deoxyadenosylcobalamin
-
shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments, situated in the Rossmann domain in the crystal structure, and separated from pyridoxal 5'-phosphate
5'-deoxyadenosylcobalamin
-
shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments
5'-deoxyadenosylcobalamin
-
dependent on
5'-deoxyadenosylcobalamin
-
dependent on
adenosylcobalamin
-
-
adenosylcobalamin
-
Km value 6.1 mM, in presence of S-subunit of D-ornithine aminomutase, Km value 3.5 mM, in presence of ATP and S-subunit of D-ornithine aminomutase, Km value 1.9 mM
adenosylcobalamine
-
-
ATP
-
or phosphonic acid analogs, stimulates, allosteric effector
Cobalamin
-
required, directly involved in the catalysis of the amino group migration
Cobalamin
-
coenzyme serves as carrier of the hydrogen that is transferred
pyridoxal 5'-phosphate
-
required
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
Km value 3.9 mM, in presence of S-subunit of D-ornithine aminomutase, Km value 3.0 mM, in presence of ATP and S-subunit of D-ornithine aminomutase, Km value 2.4 mM
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
dependent on, molecular modeling in the reaction
pyridoxal 5'-phosphate
-
stabilizes high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons, bound at the top of the TIM barrel domain and separated from 5'-deoxyadenosylcobalamin, binding site structure involving residues Tyr263, Asn299, Arg184, Arg268, Ser189, Gly187, Gln188, and Ser189, overview
pyridoxal 5'-phosphate
-
stabilizes high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons
pyridoxal 5'-phosphate
-
dependent on
pyridoxal 5'-phosphate
-
dependent on
FAD
-
slight activation
additional information
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
-
additional information
-
the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal-5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
K+
-
stimulation by monovalent cations, K+ or NH4+
Mg2+
-
required
Mg2+
-
stimulates
NH4+
-
stimulation by monovalent cations, K+ or NH4+
Zn2+
-
purified KamDE contains a substantial quantity of metal ions, primarily Zn2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1,4-diaminobutane
-
-
1-Aminoproline
-
D- and L-form
2-Amino-n-butanoate
-
-
2-amino-n-pentanoic acid
-
-
2-aminoisobutanoate
-
-
3,5-diaminohexanoate
-
-
3-amino-n-butanoate
-
-
3-aminoisobutanoate
-
-
4-amino-n-butanoate
-
-
4-thia-D-lysine
-
suicide inhibitor
4-thia-L-lysine
-
suicide inhibitor
6-Amino-n-hexanoic acid
-
-
DL-delta-hydroxylysine
-
-
DL-epsilon-N-Acetyllysine
-
-
glycoprotein intrinsic factor
-
-
-
Isonicotinic acid hydrazide
-
-
L-2,4-diamino-n-butyrate
-
-
N-Acetylimidazole
-
-
S-aminoethylcysteine
-
-
Tetranitromethane
-
-
additional information
-
homologues of substrate D-lysine, D-2,5-diaminopentanoic acid, 2,4-diaminobutyric acid, and D-2,3-diaminopropionic acid bind to pyridoxal 5'-phosphate as an external aldimine and elicit the 5'-deoxyadenosylcobalamin Co-C bond homolysis and the accumulations of cob(II)alamin and analogue-based radicals. The position for hydrogen atom abstraction from D-2,5-diaminopentanoic acid and 2,4-diaminobutyric acid by the 5'-deoxyadenosyl radical occurs at the carbon adjacent to the imine, resulting in overstabilized radicals by spin delocalization through the imine into the pyridine ring of pyridoxal 5'-phosphate. These radicals block the active site, inhibit the enzyme, and poise the enzyme into two distinct conformations: for even-numbered analogues, the cob(II)alamin remains proximal to and spin-coupled with the analogue-based radical in the closed state while odd-numbered analogues trigger the transition to the open state of the enzyme, inactivation mechanism, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
ATP
-
protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 128000 Da subunit, but ATP no longer has a regulatory effect on it. The S subunit of D-ornithine aminomutase, OraS, is capable of forming a complex with KamDE and restores the enzyme’s ATP-dependent allosteric regulation. ATP lowers the Km value of the KamDE-OraS complex for adenosylcobalamin and pyridoxal phosphate
mercaptan
-
e.g. 1,4-dimercaptothreitol required
mercaptan
-
required
additional information
-
presence of enzyme component E2 in the assay mixture induces ATP to activate enzyme component E1 allosterically
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.02
-
D-Lysine
-
pH and temperature not specified in the publication
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.63
-
D-Lysine
-
pH and temperature not specified in the publication
1531
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
9
9.2
-
Tris/HCl buffer
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
8
10.5
-
pH 8.0: about 55% of maximal activity, pH 10.5: about 65% of maximal activity, no activity at pH 7
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
enzyme assay
PDB
SCOP
CATH
ORGANISM
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
250000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
tetramer
-
alpha2,beta2, 2 * 55000 + 2 * 30000, SDS-PAGE; alpha2,beta2, 2 * 57261 + 2 * 29191, deduced from nucleotide sequence
tetramer
-
2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2
tetramer
-
alpha2beta2
heterotetramer
-
alpha2beta2
additional information
-
protein KamDE comprised of the 30 and 51 kDa subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 12.8 kDa subunit, but ATP no longer has a regulatory effect on it. The S subunit of D-ornithine aminomutase, OraS, is capable of forming a complex with KamDE and restores the enzyme’s ATP-dependent allosteric regulation
additional information
-
the enzyme comprises two protein components, the core enzyme E1 and an auxiliary activating protein E2. E1 is a 170 kDa heterotetramer composed of 55 kDa alpha-subunits and 30 kDa beta-subunits and formulated as alpha2beta2, whereas the molecular mass of E2 is about 80 kDa. E2 shows dAdoCbl synthetase activity when isolated separately. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
crystal structure analysis
-
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
-
-
dissociation of complex
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
35
55
-
approx. 50% loss of activity at 43°C after 5 min, almost complete loss of activity at 55°C after 5 min
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
inactivated by irradiation
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-15°C, Tris buffer, pH 8.5-9.0, protein concentration of no less than 3 mg/ml, 20-40% loss of activity after 1 month
-
-20°C, 50% glycerol, protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase can be stored for several months with significant loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase, expression in Escherichia coli
-
recombinant and native KamDE
-
recombinant enzyme from Escherichia coli
-
recombinant 5,6-LAM
-
recombinant enzyme from Escherichia coli
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
enzyme expression in Escherichia coli
-
expression in Escherichia coli
-
genes kamDE coding for the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase, expression in Escherichia coli
-
enzyme expression in Escherichia coli
-
expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Y263F
-
the mutation abolishes the enzymatic activity
C235S
-
9% of wild-type activity
K144Q
-
no activity
K23Q
-
75% of wild-type activity
K377Q
-
0.6% of wild-type activity
K446Q
-
25% of wild-type activity
K58Q
-
33% of wild-type activity
K90Q
-
72% of wild-type activity
additional information
-
protein KamDE comprised of the 30000 and 51000 kDa subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 12800 kDa subunit, but ATP no longer has a regulatory effect on it. The S subunit of D-ornithine aminomutase, OraS, is capable of forming a complex with KamDE and restores the enzyme’s ATP-dependent allosteric regulation. OraS protein alone lowers the Km of KamDE for adenosylcobalamin and pyridoxal phosphate