Information on EC 2.6.1.102 - GDP-perosamine synthase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.6.1.102
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RECOMMENDED NAME
GeneOntology No.
GDP-perosamine synthase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
GDP-alpha-D-perosamine + 2-oxoglutarate = GDP-4-dehydro-alpha-D-rhamnose + L-glutamate
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Amino sugar and nucleotide sugar metabolism
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GDP-D-perosamine biosynthesis
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d-mannose degradation
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SYSTEMATIC NAME
IUBMB Comments
GDP-4-amino-4,6-dideoxy-alpha-D-mannose:2-oxoglutarate aminotransferase
A pyridoxal 5'-phosphate enzyme. D-Perosamine is one of several dideoxy sugars found in the O-specific polysaccharide of the lipopolysaccharide component of the outer membrane of Gram-negative bacteria. The enzyme catalyses the final step in GDP-alpha-D-perosamine synthesis.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + L-glutamate
GDP-4-amino-3,4,6-trideoxy-alpha-D-mannose + 2-oxoglutarate
show the reaction diagram
GDP-4-dehydro-6-deoxy-alpha-D-mannose + L-glutamate
GDP-4-amino-4,6-dideoxy-alpha-D-mannose + 2-oxoglutarate
show the reaction diagram
GDP-4-dehydro-6-deoxy-D-mannose + L-glutamate
GDP-alpha-D-perosamine + 2-oxoglutarate
show the reaction diagram
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-
-
-
?
GDP-4-dehydro-6-deoxy-D-mannose + L-glutamate
GDP-D-perosamine + 2-oxoglutarate
show the reaction diagram
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-
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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
GDP-4-dehydro-6-deoxy-alpha-D-mannose + L-glutamate
GDP-4-amino-4,6-dideoxy-alpha-D-mannose + 2-oxoglutarate
show the reaction diagram
GDP-4-dehydro-6-deoxy-D-mannose + L-glutamate
GDP-alpha-D-perosamine + 2-oxoglutarate
show the reaction diagram
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?
GDP-4-dehydro-6-deoxy-D-mannose + L-glutamate
GDP-D-perosamine + 2-oxoglutarate
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
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optimal concentration is 20 mM
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
GDP-4-dehydro-6-deoxy-alpha-D-mannose
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pH 7.5, 22°C
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
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pyridoxal 5'-phosphate dependent aminotransferase
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016
GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose
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pH 7.5, 22°C
0.013 - 0.06
GDP-4-dehydro-6-deoxy-alpha-D-mannose
0.07 - 0.09
GDP-4-dehydro-6-deoxy-D-mannose
0.1 - 4.6
L-glutamate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.015
GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose
Caulobacter vibrioides
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pH 7.5, 22°C
2.7
GDP-4-dehydro-6-deoxy-alpha-D-mannose
Caulobacter vibrioides
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pH 7.5, 22°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
208
GDP-4-dehydro-6-deoxy-alpha-D-mannose
Caulobacter vibrioides
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pH 7.5, 22°C
7757
210
GDP-4-dehydro-6-deoxy-D-mannose
Escherichia coli
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pH and temperature not specified in the publication
4524
52
L-glutamate
Escherichia coli
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pH and temperature not specified in the publication
41
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 8
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GDP-4-dehydro-6-deoxy-alpha-D-mannose, pH 8, 37°C, His-tag RfbE fusion protein
42
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L-glutamate, pH 8, 37°C, His-tag RfbE fusion protein
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
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assay at
PDB
SCOP
CATH
ORGANISM
UNIPROT
Caulobacter crescentus (strain ATCC 19089 / CB15)
Caulobacter crescentus (strain ATCC 19089 / CB15)
Caulobacter crescentus (strain ATCC 19089 / CB15)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40900
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4 * 40900, SDS-PAGE
44330
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10 * 44330, His-tag PerA, SDS-PAGE
170000
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gel filtration
431000
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recombinant His-tagged Per fusion protein
458000
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His-tag PerA, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop method of vapor diffusion using a sparse matrix screen. Two crystal structures: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 A resolution, respectively
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the three-dimensional structure of the enzyme is determined to a nominal resolution of 1.8 A and refined to an R-factor of 17.9%. Each subunit of the dimeric enzyme contains a seven-stranded mixed beta-sheet, a two-stranded antiparallel beta-sheet, and 12 alpha-helices
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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His-tag PerA holds 55% residual activity after 20 min incubation
60
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His-tag PerA, 10 min, completely inactivated
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 30 days, His-tag PerA, residual activity of 68%
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
His-tagged fusion protein
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression as a His-tagged fusion protein in Escherichia coli BL21
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expression in Escherichia coli BL21 (DE3)
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overexpression in Escherichia coli BL21 (DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE