Information on EC 6.3.5.9 - hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
6.3.5.9
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RECOMMENDED NAME
GeneOntology No.
hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 ATP + hydrogenobyrinic acid + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + hydrogenobyrinic acid a,c-diamide + 2 L-glutamate
show the reaction diagram
This step in the aerobic biosynthesis of cobalamin generates hydrogenobyrinic acid a,c-diamide, the substrate required by EC 6.6.1.2, cobaltochelatase, which adds cobalt to the macrocycle
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)
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vitamin B12 metabolism
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Porphyrin and chlorophyll metabolism
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Metabolic pathways
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SYSTEMATIC NAME
IUBMB Comments
hydrogenobyrinic-acid:L-glutamine amido-ligase (AMP-forming)
This step in the aerobic biosynthesis of cobalamin generates hydrogenobyrinic acid a,c-diamide, the substrate required by EC 6.6.1.2, cobaltochelatase, which adds cobalt to the macrocycle.
CAS REGISTRY NUMBER
COMMENTARY hide
132053-22-6
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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
5'-deoxy-5'-adenosyl-cobyrinic acid + 2 ATP + 2 glutamine + 2 H2O
5'-deoxy-5'-adenosyl-cobyrinic acid ac-diamide + 2 ADP + 2 phosphate + 2 glutamate
show the reaction diagram
5'-deoxy-5'-adenosyl-cobyrinic acid + ATP + ammonia + H2O
5'-deoxy-5'-adenosyl-cobyrinic acid ac-diamide + ADP + phosphate + ?
show the reaction diagram
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?
adenosyl-cobyrinic acid pentaamide + ATP + glutamine + H2O
ADP + glutamate + phosphate + ?
show the reaction diagram
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?
adenosyl-cobyrinic acid tetraamide + ATP + glutamine + H2O
ADP + glutamate + phosphate + ?
show the reaction diagram
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?
adenosyl-cobyrinic acid triamide + ATP + glutamine + H2O
ADP + glutamate + phosphate + ?
show the reaction diagram
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?
alpha-ribazole + phosphate
N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole + H2O
show the reaction diagram
ATP + (aq)2cobyrinic acid + glutamine + H2O
ADP + phosphate + ?
show the reaction diagram
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?
ATP + (CN,aq)cobyrinic acid + glutamine + H2O
ADP + phosphate + c-monoamide + ?
show the reaction diagram
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?
ATP + (CN,aq)cobyrinic acid -monoamide + glutamine + H2O
ADP + phosphate + ?
show the reaction diagram
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?
ATP + cobyrinic acid + ammonia + H2O
ADP + phosphate + ?
show the reaction diagram
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?
ATP + cobyrinic acid + L-glutamine + H2O
ADP + phosphate + cobyrinic acid a,c-diamide + L-glutamate
show the reaction diagram
ATP + hydrogenobyrinic acid + L-glutamine + H2O
ADP + phosphate + hydrogenobyrinic acid a,c-diamide + L-glutamate
show the reaction diagram
ATP + hydrogenobyrinic acid c-monoamide + L-glutamine + H2O
ADP + phosphate + ?
show the reaction diagram
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?
cobyrinic acid + ATP + glutamine
cobyrinic acid a,c-diamide + ADP + phosphate + glutamate
show the reaction diagram
cobyrinic acid + ATP + NH4+
cobyrinic acid a,c-diamide + ADP + phosphate
show the reaction diagram
cobyrinic acid c-monoamide + ATP + glutamine
cobyrinic acid a,c-diamide + ADP + phosphate + glutamate
show the reaction diagram
cobyrinic acid c-monoamide + ATP + NH4+
cobyrinic acid a,c-diamide + ADP + phosphate
show the reaction diagram
DMB + nicotinic acid mononucleotide
DMB-ribose-5'-phosphate
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5'-deoxy-5'-adenosyl-cobyrinic acid + 2 ATP + 2 glutamine + 2 H2O
5'-deoxy-5'-adenosyl-cobyrinic acid ac-diamide + 2 ADP + 2 phosphate + 2 glutamate
show the reaction diagram
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cobalamin biosynthetic pathway
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?
ATP + cobyrinic acid + L-glutamine + H2O
ADP + phosphate + cobyrinic acid a,c-diamide + L-glutamate
show the reaction diagram
P21632
cobalamin pathway from cobyrinic acid
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?
ATP + hydrogenobyrinic acid + L-glutamine + H2O
ADP + phosphate + hydrogenobyrinic acid a,c-diamide + L-glutamate
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25
(aq)2cobyrinic acid
pH 7.6, 30°C
0.16
(CN,aq)cobyrinic acid
pH 7.6, 30°C
0.071
(CN,aq)cobyrinic acid c-monoamide
pH 7.6, 30°C
0.00104
adenosyl-cobyrinic acid a,c-diamide
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pH 7.5, 20°C
0.00125
adenosyl-cobyrinic acid pentaamide
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pH 7.5, 20°C
0.00121
adenosyl-cobyrinic acid tetraamide
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pH 7.5, 20°C
0.00122
adenosyl-cobyrinic acid triamide
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pH 7.5, 20°C
0.012 - 20
ammonia
0.0027 - 0.12
ATP
0.00074
cobyrinic acid
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pH 7.7, wild-type enzyme
0.0003 - 0.011
cobyrinic acid c-monoamide
0.0203 - 0.053
glutamine
0.00041
Hydrogenobyrinic acid
pH 7.6, 30°C
0.00021
hydrogenobyrinic acid c-monoamide
pH 7.6, 30°C
0.033 - 0.064
L-glutamine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.16
cobyrinic acid
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pH 7.7, wild-type enzyme
0.008 - 0.2
cobyrinic acid c-monoamide
0.16
glutamine
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pH 7.7, wild-type enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.068
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adenosyl-cobyrinic acid a,c-diamide as substrate
0.083
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adenosyl-cobyrinic acid pentaamide as substrate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glycerol and DTT are necessary to stabilize the enzyme during purification
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 0.1 M Tris hydrochloride, pH 7.5, 100% activity is lost after 48 h
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-20°C, enzyme can be stored in the eluate from purification step v without detectable loss of activity
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0°C, 0.1 M Tris hydrochloride, pH 7.5, 100% activity is lost after 48 h
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloned, sequenced and overexpressed
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expression of wild-type and mutant enzymes in Escherichia coli
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identification of the structural gene
plasmid pXL 191 is transferre from Escherichia coli MC1060 to Pseudomonas denitrificans SC510 RifT through conjugation
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D45N
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less than 0.2% of amidation activity with glutamine and with NH4+, compared to wild-type values
D48N
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less than 0.3% of amidation activity with glutamine and with NH4+, compared to wild-type values
D97N
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32.4% of wild-type amidation activity with glutamine, 16.5% of wild-type amidation activity with NH4+
E90Q
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less than 0.02% of amidation activity with glutamine and with NH4+, compared to wild-type values
L47A
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10.6% of wild-type amidation activity with glutamine, 44% of wild-type amidation activity with NH4+, mutation specifically decreases the affinity of the enzyme to the cobyrinic acid c-monoamide
Y46A
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3.8% of wild-type amidation activity with glutamine, 2% of wild-type amidation activity with NH4+, mutation specifically decreases the affinity of the enzyme to the cobyrinic acid c-monoamide
D45N
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less than 0.2% of amidation activity with glutamine and with NH4+, compared to wild-type values
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D48N
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less than 0.3% of amidation activity with glutamine and with NH4+, compared to wild-type values
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D97N
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32.4% of wild-type amidation activity with glutamine, 16.5% of wild-type amidation activity with NH4+
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E90Q
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less than 0.02% of amidation activity with glutamine and with NH4+, compared to wild-type values
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Y46A
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3.8% of wild-type amidation activity with glutamine, 2% of wild-type amidation activity with NH4+, mutation specifically decreases the affinity of the enzyme to the cobyrinic acid c-monoamide
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Show AA Sequence (2529 entries)
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