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Information on EC 2.7.1.30 - glycerol kinase and Organism(s) Escherichia coli and UniProt Accession P0A6F3
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2.7.1.30 glycerol kinaseIUBMB Comments
Glycerone and L-glyceraldehyde can act as acceptors; UTP (and, in the case of the yeast enzyme, ITP and GTP) can act as donors.
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Word Map
- 2.7.1.30
- glycerol-3-phosphate
- triglyceride
- adrenal
- hypoplasia
- dystrophy
- muscular
- adipose
- 3-phosphate
-
duchenne
- lipase
- phosphoenolpyruvate
- hexokinase
-
x-linked
- dihydroxyacetone
-
contiguous
- adipocytes
- triacylglycerols
-
carboxykinase
- congenita
-
gluconeogenesis
- glycerophosphate
-
lipolysis
- hpr
- iiaglc
- 1,6-bisphosphate
- hypogonadism
-
co-immobilized
-
phosphocarrier
-
glyceroneogenesis
-
hypogonadotropic
- glycosomes
-
dissimilation
- triolein
- 1,3-propanediol
-
glucose-specific
-
aquaglyceroporins
- d-glyceraldehyde
-
phosphoenolpyruvate:sugar
- dhap
-
phosphoenolpyruvate-dependent
- sn-glycerol-3-phosphate
- sn-glycerol
- drug development
- diagnostics
- synthesis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
glycerol kinase, glycerokinase, astp, tk-gk, glycerol kinase 5, tbggk, glycerol kinase 2, atp-stimulated glucocorticoid-receptor translocation promoter, atp:glycerol 3-phosphotransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ASTP
-
-
-
-
ATP-stimulated glucocorticoid-receptor translocation promoter
-
-
-
-
ATP:glycerol 3-phosphotransferase
-
-
-
-
ATP:glycerol-3-phosphotransferase
-
-
-
-
GK
glyceric kinase
-
-
-
-
glycerokinase
-
-
-
-
kinase, glycerol (phosphorylating)
-
-
-
-
GK
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + glycerol = ADP + sn-glycerol 3-phosphate
fructose 1,6-diphosphate regulates equilibrium of dimer-tetramer, mechanism of inhibition
ATP + glycerol = ADP + sn-glycerol 3-phosphate
ordered mechanism with glycerol as the first substrate to bind
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:glycerol 3-phosphotransferase
Glycerone and L-glyceraldehyde can act as acceptors; UTP (and, in the case of the yeast enzyme, ITP and GTP) can act as donors.
CAS REGISTRY NUMBER
COMMENTARY
9030-66-4
-
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
ATP + D-glyceraldehyde
ADP + D-glyceraldehyde 3-phosphate
-
-
-
-
?
ATP + dihydroxyacetone
ADP + dihydroxyacetone phosphate
-
-
-
-
?
ATP + L-glyceraldehyde
ADP + L-glyceraldehyde 3-phosphate
-
-
-
-
?
ATP + glycerol
?
-
enzyme functions primarily in the utilization of glycerol as a carbon and energy source
-
-
?
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
-
-
-
?
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
high specificity for ATP, no other ribonucleoside triphosphate utilized
-
-
ir
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
high specificity for ATP, no other ribonucleoside triphosphate utilized
i.e. L-alpha-glycerophosphate
?
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
enzyme can utilize only ATP as phosphoryl group donor
-
-
?
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
key enzyme of glycerol metabolism in bacteria, phosphorylation of glycerol prevents diffusion through membrane
-
-
?
additional information
?
-
-
D-glyceraldehyde promotes conversion of ATP to ADP + phosphate
-
-
?
additional information
?
-
-
overview: enzyme catalyzes the phosphorylation of 28 nitrogen-, sulfur- and alkyl-substituted analogues of glycerol, phosphorylated products have stereochemistry analogous to that of sn-glycerol 3-phosphate
-
-
?
additional information
?
-
-
phosphate rather than D-glyceraldehyde 3-phosphate is formed, the hydrated form of this triose is phosphorylated in position 1 to yield an unstable intermediate that decomposes to D-glyceraldehyde + phosphate
-
-
?
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
ATP + glycerol
ADP + sn-glycerol 3-phosphate
-
key enzyme of glycerol metabolism in bacteria, phosphorylation of glycerol prevents diffusion through membrane
-
-
?
ATP + glycerol
?
-
enzyme functions primarily in the utilization of glycerol as a carbon and energy source
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system
-
-
phosphocarrier protein IIAGlc
the unphosphorylated form of the phosphocarrier protein IIAGlc is an allosteric inhibitor of Escherichia coli glycerol kinase
-
cytosolic subunit of the glucose-specific phosphotransferase system
-
allosteric inhibition
-
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
-
allosteric inhibitor
-
L-alpha-glycerophosphate
-
no inhibition up to 3 mM in presence of 0.1 M glycerol
additional information
-
regulation of activity by allosteric inhibition through complex formation with enzyme IIAGlc
-
fructose 1,6-diphosphate
-
normal enzyme is inhibited, genetically altered enzyme not, inhibition is reduced by high pH, high ionic strength or 0.2 M guanidine HCl
N-ethylmaleimide
-
protection by: glycerol propane-1,2-diol, ATP, ADP, AMP, cAMP, no protection by: Mg2+, fructose 1,6-bisphosphate, propane-1,3-diol
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
assay at 25°C, increasing pH or decreasing temperature rises Km for glycerol
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.001 - 0.01
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
-
0.001
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
Escherichia coli
-
E478C mutant protein
-
0.001
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
Escherichia coli
-
in the presence of ZnCl2
-
0.01
glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
Escherichia coli
-
wild-type protein
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.8 - 10.5
-
pH 6.8: about 30% of maximum activity, pH 10.5: about 80% of maximum activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. Reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase, EgsA/AraM), which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase, GpsA and GlpA/GlpD), and glycerol kinase (GlpK), which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, phylogenetic analyses suggest that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). The Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquires G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane. Detailed overview
metabolism
overview of the stereospecific biosynthetic pathways of glycerol 1-phosphate (G1P) and glycerol 3-phosphate (G3P)
physiological function
glycerol kinase (GlpK) is responsible for sn-glycerol 3-phosphate (G3P) synthesis
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
113000
light scattering, dimer peak in the absence of fructose 1,6-bisphosphate, G230D mutant
127000
light scattering, dimer peak in the presence of fructose 1,6-bisphosphate, G230D mutant
177000
light scattering, dimer peak in the absence of fructose 1,6-bisphosphate, wild type enzyme
227000
light scattering, tetramer peak (about 2% of the principal peak) in the absence of fructose 1,6-bisphosphate, G230D mutant
391000
light scattering, tetramer peak (about 9% of the principal peak) in the absence of fructose 1,6-bisphosphate, wild type enzyme
60000
-
2 or 4 * 60000, in solution, the enzyme exists in a dimer-tetramer equilibrium
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
light scattering analysis confirmed G230D is a dimer and is resistant to tetramer formation in the presence of fructose 1,6-bisphosphate, whereas the wild type enzyme dimers are converted into putatively inactive tetramers in the presence of fructose 1,6-bisphosphate.
homotetramer
dimer-tetramer equilibrium in solution, tetramer in the crystal
dimer or tetramer
-
2 or 4 * 60000, in solution, the enzyme exists in a dimer-tetramer equilibrium
tetramer
tetramer
-
4 * 55000-57000, equilibrium ultracentrifugation in presence of 6 M guanidine HCl, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with glycerol, in presence and absence of fructose 1,6-diphosphate, mechanism
the crystal structure of glycerol kinase mutant G230D is determined to 2.0 A resolution using a microfluidics based crystallization platform
using modified microfluidic scale-up diffraction device, crystals form after one week at ambient temperature unter crystallization conditions 0.3 M magnesium chloride, 0.1 M TrisHCl (pH 8.5), and 20% PEG 1500. Using vapor diffusion crystallization, crystals appear after one week at ambient temperature using the crystallization conditions 0.1 M magnesium chloride, 0.1 M TrisHCl (pH 8.5), and 10% PEG 1500. Glycerol kinase of the mutant G230D crystallied in space group P21 with two tetramers of 222 point symmetry in the asu. The average B factor for the overall structure of the G230D mutant is 21.2 A2.
of wild type and mutant A65T, both in complex with glycerol and ADP, and of mutant I474D, in complex with IIAGlc
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A65T
oligomeric interactions are disturbed by the amino acid substitution
G230D
I474A
the maximum extent of IIAGlc inhibition is reduced for the mutant enzyme
I474C
the maximum extent of IIAGlc inhibition is reduced for the mutant enzyme
R369A
oligomeric interactions are disturbed by the amino acid substitution
R479A
the maximum extent of IIAGlc inhibition is reduced for the mutant enzyme
R479C
the maximum extent of IIAGlc inhibition is reduced for the mutant enzyme
D72V
-
the catalytic properties of the mutant differ little from those of the wild type enzyme. The mutant shows 14.76% expression compared to the wild type enzyme
E478C
-
mutation increases the affinity for glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))
E478C/T428V/R429N
-
T428V and R429N replace two coupling locus amino acids with those from Haemophilus influenzae glycerol kinase
G427D/T428V/R429N
-
replacement of all three of the coupling locus amino acids with those from Haemophilus influenzae glycerol kinase
M271I
-
the mutant shows strongly increased Km for ATP and 30.75% expression compared to the wild type enzyme
Q37P
-
the mutant shows strongly increased Km for ATP and 65.73% expression compared to the wild type enzyme
V61L
-
the catalytic properties of the mutant differ little from those of the wild type enzyme. The mutant shows 12.71% expression compared to the wild type enzyme
G230D
structural analysis reveal that the decreased allosteric regulation in the G230D mutant is a result of the altered fructose 1,6-bisphosphate binding loop conformations in the mutant that interfere with the wild-type fructose 1,6-bisphosphate binding site. The altered fructose 1,6-bisphosphate binding loop conformation in the G230D mutant of glycerol kinase are supported through a series of intramolecular loop interactions. The appearence of Asp230 in the fructose 1,6-bisphosphate binding loops also repositions the wildtype fructose 1,6-bisphosphate binding residues away from the fructose 1,6-bisphosphate binging site.
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5
-
0°C, 24 h, complete loss of activity, 30°C, 30 min, 75% loss of activity
641287
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
70
additional information
60
-
in presence of 10 mM glycerol and 1 mM EDTA almost all glycerol kinases can be heated for prolonged periods
additional information
-
normal and mutant enzyme stabilized against heat inactivation by glycerol, but not by fructose 1,6-bisphosphate
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glycerol, 0.01 M, EDTA, 0.001 M and 0.001 M 2-mercaptoethanol prevent inactivation during purification
-
normal and mutant enzyme stabilized against heat inactivation by glycerol, but not by fructose 1,6-bisphosphate
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, suspension of crystals, 10 mM glycerol, 1 mM EDTA, 1 mM 2-mercaptoethanol, 0.1 M potassium phosphate, pH 7.0, saturated with ammonium sulfate, stable for several years
-
as crystalline suspension in saturated ammonium sulfate, solutions containing 10 mM glycerol, 1 mM EDTA and a thiol e.g. 2-mercaptoethanol, yeast enzyme stable for several months, E. coli enzyme for several years
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
metal-chelate affinity chromatography using a Ni-NTA column, anion exchange chromatography using a Mono Q 5/50 GL column and gel filtration chromatography using s Superdex 200 10/30 GL column,all purification steps are performed in standard buffer (20 mM TrisHCl (pH 7.5), 10 mM glycerol, 1 mM beta-mercaptoethanol) at 4°C excluding the affinity chromatography purification
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Thorner, J.W.; Paulus, H.
Glycerol and glycerate kinases
The Enzymes,3rd ed. (Boyer,P. D. ,ed. )
8
487-508
1973
Gluconobacter oxydans, Klebsiella aerogenes, Bacillus subtilis, Bombus sp., Bos taurus, Saccharomyces cerevisiae, Candida mycoderma, Wickerhamomyces anomalus, Cyberlindnera jadinii, Cavia porcellus, Gallus gallus, Clostridium novyi, Columba sp., Oryctolagus cuniculus, Escherichia coli, Enterococcus faecalis, Felis catus, Geotrichum candidum, Halobacterium salinarum, Homo sapiens, Locusta sp., Mesocricetus auratus, Staphylococcus aureus, Mycobacterium tuberculosis, Mus musculus, Mycobacterium sp., Mycobacterium butyricum, Mycolicibacterium smegmatis, Neurospora crassa, Nocardia asteroides, Pseudomonas aeruginosa, Rattus norvegicus, Shigella sonnei, trout, Mycobacterium sp. 607
-
Hayashi, S.; Lin, E.C.C.
Purification and properties of glycerol kinase from Escherichia coli
J. Biol. Chem.
242
1030-1035
1967
Escherichia coli
Crans, D.C.; Whitesides, G.M.
Glycerol kinase: substrate specificity
J. Am. Chem. Soc.
107
7008-7018
1985
Geobacillus stearothermophilus, Saccharomyces cerevisiae, Candida mycoderma, Escherichia coli
-
Pettigrew, D.W.
Inactivation of Escherichia coli glycerol kinase by 5,5-dithiobis(2-nitrobenzoic acid) and N-ethylmaleimide: evidence for nucleotide regulatory binding sites
Biochemistry
25
4711-4718
1986
Escherichia coli
Faber, H.R.; Pettigrew, D.W.; Remington, S.J.
Crystallization and preliminary X-ray studies of Escherichia coli glycerol kinase
J. Mol. Biol.
207
637-639
1989
Escherichia coli
Kee, Y.; Lee, Y.S.; Chung, C.H.
Improved methods for purification and assay of glycerol kinase from Escherichia coli
J. Chromatogr.
428
345-351
1988
Escherichia coli
Comer, M.J.; Bruton, C.J.; Atkinson, T.
Purification and properties of glycerokinase from Bacillus stearothermophilus
J. Appl. Biochem.
1
259-270
1979
Geobacillus stearothermophilus, Candida mycoderma, Escherichia coli
-
Thorner, J.W.; Paulus, H.
Catalytic and allosteric properties of glycerol kinase from Escherichia coli
J. Biol. Chem.
248
3922-3932
1973
Escherichia coli
Yu, P.; Pettigrew, D.W.
Linkage between fructose 1,6-bisphosphate binding and the dimer-tetramer equilibrium of Escherichia coli glycerol kinase: critical behavior arising from change of ligand stoichiometry
Biochemistry
42
4243-4252
2003
Escherichia coli (P0A6F3), Escherichia coli
Mao, C.; Ozer, Z.; Zhou, M.; Uckun, F.M.
X-Ray structure of glycerol kinase complexed with an ATP analog implies a novel mechanism for the ATP-dependent glycerol phosphorylation by glycerol kinase
Biochem. Biophys. Res. Commun.
259
640-644
1999
Escherichia coli
Feese, M.D.; Faber, H.R.; Bystrom, C.E.; Pettigrew, D.W.; Remington, S.J.
Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation
Structure
6
1407-1418
1998
Escherichia coli
Pettigrew, D.W.; Liu, W.Z.; Holmes, C.; Meadow, N.D.; Roseman, S.
A single amino acid change in Escherichia coli glycerol kinase abolishes glucose control of glycerol utilization in vivo
J. Bacteriol.
178
2846-2852
1996
Escherichia coli, Escherichia coli C.Lin 43
Ormo, M.; Bystrom, C.E.; Remington, S.J.
Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate
Biochemistry
37
16565-16572
1998
Escherichia coli (P0A6F3), Escherichia coli
Yeh, J.I.; Charrier, V.; Paulo, J.; Hou, L.; Darbon, E.; Claiborne, A.; Hol, W.G.; Deutscher, J.
Structures of enterococcal glycerol kinase in the absence and presence of glycerol: correlation of conformation to substrate binding and a mechanism of activation by phosphorylation
Biochemistry
43
362-373
2004
Escherichia coli, Enterococcus casseliflavus
Stefuca, V.; Vostiar, I.; Sefcovicova, J.; Katrlik, J.; Mastihuba, V.; Greifova, M.; Gemeiner, P.
Development of enzyme flow calorimeter system for monitoring of microbial glycerol conversion
Appl. Microbiol. Biotechnol.
72
1170-1175
2006
Cellulomonas sp., Escherichia coli
Anderson, M.J.; DeLabarre, B.; Raghunathan, A.; Palsson, B.O.; Brunger, A.T.; Quake, S.R.
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices
Biochemistry
46
5722-5731
2007
Escherichia coli (P0A6F3), Escherichia coli
Yu, P.; Lasagna, M.; Pawlyk, A.C.; Reinhart, G.D.; Pettigrew, D.W.
IIAGlc inhibition of glycerol kinase: a communications network tunes protein motions at the allosteric site
Biochemistry
46
12355-12365
2007
Escherichia coli (P0A6F3), Escherichia coli
Pettigrew, D.W.
Amino acid substitutions in the sugar kinase/hsp70/actin superfamily conserved ATPase core of E. coli glycerol kinase modulate allosteric ligand affinity but do not alter allosteric coupling
Arch. Biochem. Biophys.
481
151-156
2009
Escherichia coli
Pettigrew, D.W.
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase
Arch. Biochem. Biophys.
492
29-39
2009
Escherichia coli (P0A6F3), Escherichia coli
Applebee, M.K.; Joyce, A.R.; Conrad, T.M.; Pettigrew, D.W.; Palsson, B.O.
Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli
J. Biol. Chem.
286
23150-23159
2011
Escherichia coli
Yokobori, S.I.; Nakajima, Y.; Akanuma, S.; Yamagishi, A.
Birth of archaeal cells molecular phylogenetic analyses of G1P dehydrogenase, G3P dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having G1P polar lipids
Archaea
2016
1802675
2016
Escherichia coli (P0A6F3)
EXTERNAL LINKS (specific for EC-Number 2.7.1.30)
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