Information on EC 2.7.1.30 - glycerol kinase

-

-

-

Drosophila melanogaster

there are five glycerol kinase-like genes in Drosophila melanogaster. The locus CG18374, located at 61B2, is the closest homolog to the X-linked glycosyl kinase gene in Homo sapiens, sharing 53% identity. Another close homolog CG7995 (located at 62B1) shares 48% homology to the human glycerol kinase. Three other loci CG1271 at 63A3, CG1216 at 61B2, and CG8298 at 48D5 do not share the same degree of homology. Most key functional residues are missing in CG1216 suggesting it has no glycerol kinase activity.; there are five glycerol kinase-like genes in Drosophila melanogaster.

681943

-

-

641318, 641324, 641328

-

Enterobacter aerogenes

-

-

-

661122, 677308, 702293

-

Enterococcus faecalis

-

-

Epidermophyton floccosum

-

641289, 641290

-

Escherichia coli C.Lin 43

strain C.Lin 43

-

-

-

-

641287, 641292, 641310

-

-

641297, 641301, 641306, 641309

-

Geotrichum candidum

-

-

Gluconobacter oxydans

-

-

Haemophilus influenzae

-

641321

-

Halobacterium salinarum

-

-

-

-

-

-

-

-

-

-

Mycobacterium butyricum

-

-

Mycobacterium smegmatis

-

-

Mycobacterium sp.

607

-

Mycobacterium sp. 607

607

Mycobacterium tuberculosis

-

-

-

-

-

-

-

Oryctolagus cuniculus

-

-

Osmerus mordax

rainbow smelt

721260

-

Pediococcus pentosaceus

-

-

kidney bean

-

pea

-

-

705779

Uniprot

Pseudomonas aeruginosa

-

-

-

641287, 641297, 688443, 722310

-

Shigella sonnei

-

-

Staphylococcus aureus

-

-

Sus scrofa

-

641293

-

-

-

-

-

trout

-

-

-

721188

Trypanosoma brucei gambiense IL2343

UniProt

-

721188

Trypanosoma brucei ILTat1.4

UniProt

-

723070

Q9NJP9

Uniprot

Trypanosoma congolense

-

723070

Q75T26

UniProt

Trypanosoma congolense IL1180

-

UniProt

-

UniProt

Trypanosoma vivax IL1392

-

UniProt

broad bean

-

Vigna radiata var. radiata

-

-

Wickerhamomyces anomalus

-

-

Zea mays

-

-

malfunction

metabolism

-

the enzyme plays an essential role in central and lipid metabolism

723091

physiological function

ADP + sn-glycerol 3-phosphate

ATP + glycerol

8 entries

ATP + 1,3-propanediol

ADP + ?

Candida mycoderma

-

weak

641305

-

?

ATP + 1-deoxy-sn-glycerol

ADP + ?

Candida mycoderma

-

-

?

ATP + 2-deoxyglycerol

ADP + ?

Candida mycoderma

-

-

?

ATP + 2-mercaptoethanol

ADP + ?

Candida mycoderma

-

641302

-

?

ATP + 2-methylglycerol

ADP + ?

Candida mycoderma

-

-

?

ATP + aminopropanediol

ADP + ?

Candida mycoderma

-

R- and S-

641302

-

?

ATP + D-glyceraldehyde

ADP + D-glyceraldehyde 3-phosphate

-

641287, 641294, 641295

-

?

ATP + dihydroxyacetone

ADP + dihydroxyacetone phosphate

ATP + dihydroxypropyl dichloroacetate

ADP + ?

-

glycerol analogue

-

?

ATP + glyceric acid

ADP + ?

-

-

?

ATP + glycerol

?

ATP + glycerol

ADP + sn-glycerol 3-phosphate

94 entries

ATP + L-glyceraldehyde

ADP + L-glyceraldehyde 3-phosphate

ATP + mercaptopropanediol

1-mercaptopropanediol 1-phosphate + ADP

ATP + monoacetin

ADP + ?

-

glycerol analogue

-

?

ATP + monobutyrin

ADP + ?

-

glycerol analogue

-

?

ATP + monothioglycerol

ADP + ?

-

-

?

CTP + glycerol

CDP + glycerol 3-phosphate

glycerol + ATP

sn-glycerol 3-phosphate + ADP

GTP + glycerol

GDP + glycerol 3-phosphate

ITP + glycerol

IDP + glycerol 3-phosphate

TTP + glycerol

TDP + glycerol 3-phosphate

Microsporum gypseum

-

-

?

UTP + glycerol

UDP + glycerol 3-phosphate

XTP + glycerol

XDP + glycerol 3-phosphate

Candida mycoderma

-

641305

-

?

additional information

?

-

9 entries

ATP + glycerol

?

ATP + glycerol

ADP + sn-glycerol 3-phosphate

ATP

(NH4)2SO4

Microsporum gypseum

-

activates

Co2+

-

best effect, may be replaced by Zn2+

KCl

Mg2+

Mn2+

Zn2+

-

can substitute for Co2+

641319

additional information

(NH4)2SO4

-

1,2-propanediol

-

1-Pentanol

-

3-Chloro-1,2-propanediol

-

3-Deoxy-sn-glycerol

Candida mycoderma

-

ADP

AMP

ATP

-

substrate inhibition

Butane-1,3-diol

Candida mycoderma

-

D- and L-configuration

CrATP

Candida mycoderma

-

coordination complex of Cr3+ and ATP, dead-end inhibitor

641305

cytosolic subunit of the glucose-specific phosphotransferase system

-

allosteric inhibition

-

D-fructose 1,6-bisphosphate

-

701931

D-fructose-1,6-bisphosphate

-

allosteric inhibition

DTNB

-

inactivation reversed by dithiothreitol

641298

erythritol

Candida mycoderma

-

ethanediol

ethanol

Candida mycoderma

-

fructose 1,6-bisphosphate

fructose 1,6-diphosphate

10 entries

glucose

11 entries

glucose 6-phosphate

9 entries

glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system

-

701931

-

glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))

-

allosteric inhibitor

701908

-

glycerol

glycerol 3-phosphate

HgCl2

-

iodoacetamide

iodoacetate

-

L(+)-Butane-2,3-diol

Candida mycoderma

-

L-alpha-glycerophosphate

-

no inhibition up to 3 mM in presence of 0.1 M glycerol

L-Threitol

Candida mycoderma

-

Mn2+

-

N-ethylmaleimide

Na2SO4

-

NaCl

-

p-chloromercuribenzoate

p-Hydroxymercuriphenylsulfonate

-

641287, 641294

phosphocarrier protein IIAGlc

-

the unphosphorylated form of the phosphocarrier protein IIAGlc is an allosteric inhibitor of Escherichia coli glycerol kinase

685101

-

Procion Blue MX-3G

-

5 mM, inactivates after a period of increased activity

641301

propan-1-ol

propan-2-ol

Salyrganic acid

Candida mycoderma

-

additional information

-

1,3-butanediol

-

activates

1,3-Propanediol

-

activates

1,4-Butanediol

-

activates

1-butanol

-

activates

1-Chloro-2-propanol

-

activates

1-propanol

2,3-Butanediol

-

activates

2-butanol

-

activates

2-Chloroethanol

-

activates

2-methyl-1-propanol

-

activates

2-Methyl-2-propanol

-

activates

2-Pentanol

-

activates

2-propanol

3-methyl-1-butanol

-

activates

Cyclohexanol

-

activates

Ethanediol methyl ether

-

activates

ethanol

-

activates

methanol

-

activates

rosiglitazone

-

rosiglitazone treatment markebly increases glycerol kinase mRNA expression in both the mesenteric and epididymal adipose tissues (1085.9% and 523.8% of the abundance in Long-Evans Tokushima Otsuka rats, respectively). The magnitude of glycerol kinase induced by rosiglitazone is significantly greater in the mesenteric fat than in the epididymal fat.

681755

45

1-deoxy-sn-glycerol

Candida mycoderma

-

88

2-deoxyglycerol

Candida mycoderma

-

0.046

2-mercaptoethanol

Candida mycoderma

-

25°C, pH 8.2

641302

5.7

2-methylglycerol

Candida mycoderma

-

0.24 - 0.69

ADP

0.006 - 3.29

ATP

19 entries

0.515

CTP

-

0.14

dichloro-monoacetin

-

pH 7.35, 37°C

0.5 - 100

dihydroxyacetone

0.15

glyceric acid

0.01 - 2

glycerol

22 entries

12.56

glycerol-3-phosphate

-

pH 7.0

641312

0.145

GTP

-

3 - 42

L-Glyceraldehyde

3.83

L-glycerol-3-phosphate

-

25°C, pH 8.0

641315

0.009 - 0.01

MgATP2-

0.169

Monoacetin

-

pH 7.35, 37°C

0.491

Monobutyrin

-

pH 7.35, 37°C

4.9

monothioglycerol

1.09 - 1.37

sn-glycerol 3-phosphate

0.62

UTP

-

additional information

25 entries

-

1670

glycerol

Candida mycoderma

-

250

propan-1-ol

Candida mycoderma

-

1500

propan-2-ol

Candida mycoderma

-

0.001 - 0.01

glucose-specific phosphocarrier protein of the phosphoenolpyruvate:glucose phosphotransferase system (IIA(Glc))

-

0.054

-

recombinant enzyme, using 1% methanol as carbon sources in the medium, at pH 9.8 and 30°C

722310

0.13

-

recombinant enzyme, using 1% glycerol and 1% methanol as carbon sources in the medium, at pH 9.8 and 30°C

722310

2

-

at pH 7.0 and 70°C

722839

15.5

for glycerol

705779

18.3

for ATP

25.2

-

41.2

-

pH 7.0, 25°C

641294

100

-

25°C

101

Candida mycoderma

-

25°C

116

-

30°C

120

-

pH 9.8, 30°C

641306

177

-

pH 7.5, 25°C

additional information

7 - 7.5

Clostridium novyi

-

7

Culex quinquefasciatus

-

and pH 10.0

641291

7 - 8

-

7 - 7.5

-

7 - 9.5

-

7

-

reverse reaction

641312

7.5

Pediococcus pentosaceus

-

8

8.5 - 9

;

8.6

-

reverse reaction

9 - 9.5

-

9

-

9 - 9.5

-

9.5

-

9.8

-

10

10.5

Epidermophyton floccosum

-

6.8 - 10.5

-

pH 6.8: about 30% of maximum activity, pH 10.5: about 80% of maximum activity

7 - 9.5

8 entries

25

28

Pediococcus pentosaceus

-

641323

30

-

assay at

37

-

assay at

50 - 70

Thermus thermophilus

-

641325

65

-

80

-

641319

30 - 80

-

30°C: about 50% of maximum activity, 80°C: about 65% of maximum activity

A-549 cell

-

lung cell line

adipocyte

Mus musculus

-

There is no difference in glycerol mRNA level between control 3T3-L1 adipocytes and 3T3-L1 Aqp7-RNAi transfected adipocytes, whereas a 4fold enzymatic activation of glycerol kinase is observable in Aqp7 knockout adipocytes (activity assay: 50 mM TrisHCl, pH 7.2, 5 mM ATP, 10 mM MgCl2, 100 mM KCl, 2.5 mM DTT, 4 mM glycerol, 500 microM 3H-glycerol, for 90 min at 37°C).

-

SS6-2 cell, stem cells from fat with myotube characteristics

-

-

Aqp7-/- knockout mice have significantly lower plasma glycerol level under 12 h fasting conditions.

-

-

newborn, expresses only isoform GK-EX18

Fanconi anemia lymphoid cell line

-

from patients with enzyme deficiency and normal individuals

cultured

-

kidney cell line

G-402 cell

-

kidney cell line, expresses only isoform GK+EX18

-

-

adult hepatoblastoma cell line

hepatocyte

-

primary culture of

hepatoma cell line

-

HaIIE (ATCC)

-

Culex quinquefasciatus

-

4th instar larvae

Candida mycoderma

-

-

-

pancreatic islets and pancreas. The glycerol kinase mRNA level in the Aqp7-/- pancreatic islets is 655% that in Aqp7+/+ islets. The glycerol activity is increased in both total pancreases and islets isolated from Aqp7-/- mice compared with those isolated from Aqp+/+ mice (tested with cell homogenates, activity assay: 50 mM Tris-HCl, pH 7.2, 5 mM ATP, 10 mM MgCl2, 100 mM KCl, 2.5 mM dithiothreitol, 4 mM glycerol, 50 microM [14C]glycerol, for 3 h at 37°C). The absence of AQP7 is associated with a moderate increase in the glycerol content of the total pancreas. There is a 2fold increase in the glycerol content of pancreatic islets isolated from Aqp7-/- mice compared with those from Aqp7+/+ mice.

-

-

expresses only isoform GK+EX18

-

-

fetal liver cell line

additional information

-

additional information

1r59, download, 3D-view

SCOPe (1r59)

CATH (1r59)

1xup, download, 3D-view

SCOPe (1xup)

CATH (1xup)

3d7e, download, 3D-view

SCOPe (3d7e)

CATH (3d7e)

3flc, download, 3D-view

SCOPe (3flc)

CATH (3flc)

3h3n, download, 3D-view

SCOPe (3h3n)

CATH (3h3n)

3h3o, download, 3D-view

SCOPe (3h3o)

CATH (3h3o)

3h45, download, 3D-view

SCOPe (3h45)

CATH (3h45)

3h46, download, 3D-view

SCOPe (3h46)

CATH (3h46)

1bo5, download, 3D-view

SCOPe (1bo5)

CATH (1bo5)

Escherichia coli (strain K12)

1bot, download, 3D-view

SCOPe (1bot)

CATH (1bot)

Escherichia coli (strain K12)

1bu6, download, 3D-view

SCOPe (1bu6)

CATH (1bu6)

Escherichia coli (strain K12)

1bwf, download, 3D-view

SCOPe (1bwf)

CATH (1bwf)

Escherichia coli (strain K12)

1gla, download, 3D-view

SCOPe (1gla)

CATH (1gla)

Escherichia coli (strain K12)

1glb, download, 3D-view

SCOPe (1glb)

CATH (1glb)

Escherichia coli (strain K12)

1glc, download, 3D-view

SCOPe (1glc)

CATH (1glc)

Escherichia coli (strain K12)

1gld, download, 3D-view

SCOPe (1gld)

CATH (1gld)

Escherichia coli (strain K12)

1gle, download, 3D-view

SCOPe (1gle)

CATH (1gle)

Escherichia coli (strain K12)

1glf, download, 3D-view

SCOPe (1glf)

CATH (1glf)

Escherichia coli (strain K12)

1glj, download, 3D-view

SCOPe (1glj)

CATH (1glj)

Escherichia coli (strain K12)

1gll, download, 3D-view

SCOPe (1gll)

CATH (1gll)

Escherichia coli (strain K12)

3ezw, download, 3D-view

SCOPe (3ezw)

CATH (3ezw)

Escherichia coli (strain K12)

2w40, download, 3D-view

SCOPe (2w40)

CATH (2w40)

2w41, download, 3D-view

SCOPe (2w41)

CATH (2w41)

4e1j, download, 3D-view

SCOPe (4e1j)

CATH (4e1j)

Rhizobium meliloti (strain 1021)

O86033

3g25, download, 3D-view

SCOPe (3g25)

CATH (3g25)

Staphylococcus aureus (strain COL)

Q5HGD2

3ge1, download, 3D-view

SCOPe (3ge1)

CATH (3ge1)

Staphylococcus aureus (strain COL)

Q5HGD2

2zf5, download, 3D-view

SCOPe (2zf5)

CATH (2zf5)

Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

O93623

3wxi, download, 3D-view

SCOPe (3wxi)

CATH (3wxi)

3wxj, download, 3D-view

SCOPe (3wxj)

CATH (3wxj)

3wxk, download, 3D-view

SCOPe (3wxk)

CATH (3wxk)

3wxl, download, 3D-view

SCOPe (3wxl)

CATH (3wxl)

5azi, download, 3D-view

SCOPe (5azi)

CATH (5azi)

5azj, download, 3D-view

SCOPe (5azj)

CATH (5azj)

45000

-

53000

-

54000 - 58000

-

gel filtration

641310

56000

-

SDS-PAGE

677400

113000

-

light scattering, dimer peak in the absence of fructose 1,6-bisphosphate, G230D mutant

120000

-

sucrose density gradient centrifugation

641308

127000

-

light scattering, dimer peak in the presence of fructose 1,6-bisphosphate, G230D mutant

140000

-

gel filtration, zone sedimentation in sucrose density gradient

158000

-

dimeric native enzyme, gel filtration

177000

-

light scattering, dimer peak in the absence of fructose 1,6-bisphosphate, wild type enzyme

200000

-

gel filtration

641328

210000 - 217000

-

equilibrium sedimentation

210000

-

gel filtration

220000

Thermus thermophilus

-

gel filtration

641325

224000

-

tetrameric native enzyme, gel filtration

227000

-

light scattering, tetramer peak (about 2% of the principal peak) in the absence of fructose 1,6-bisphosphate, G230D mutant

230000

-

gel filtration

236000

-

gel filtration

251000

Candida mycoderma

-

diffusion and sedimentation data

280000 - 300000

-

sedimentation equilibrium light scattering method

391000

-

light scattering, tetramer peak (about 9% of the principal peak) in the absence of fructose 1,6-bisphosphate, wild type enzyme

?

dimer

dimer or tetramer

-

2 or 4 * 60000, in solution, the enzyme exists in a dimer-tetramer equilibrium

homodimer

homotetramer

-

dimer-tetramer equilibrium in solution, tetramer in the crystal

701931

monomer

-

1 * 53000

641288

tetramer

10 entries

phosphoprotein

additional information

-

activity is enhanced phosphorylation of His232

702293

-

crystals are obtained by the hanging-drop technique from a solution containing 29% polyethylene glycol 400, 0.1 M sodium acetate pH 4.5, 0.1 M calcium acetate and 10% glycerol. The crystals can grow in the presence of 33% PEG 400, which allows to mount the crystals and directyl flash-cool them. Repeated flash-annealing causes a significant decrease in the averaged mosaicity along with an increase in the overall peak counts of reflections and an enhanced signal-to-noise ratio. Individual reflection-profile analysis reveales a mostly dual domain structure, showing the minimization of one domain as a result of flash-annealing.

-

677308

crystals of native and mutant enzyme with bound glycerol, hanging drop vapor diffusion method

-

661122

-

-

641294, 641295, 641300, 641317

in complex with glycerol, ADP and the allosteric effector enzyme IIAGlc

-

661122

in complex with glycerol, in presence and absence of fructose 1,6-diphosphate, mechanism

-

641326

of wild type and mutant A65T, both in complex with glycerol and ADP, and of mutant I474D, in complex with IIAGlc

-

641320

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.

-

-

705779

crystals are grown at 20°C by the sitting-drop vapour diffusion method. Native X-ray diffraction data are collected to 2.4 A resolution using synchrotron radiation at station BL44XU of SPring-8. The crystal belongs to the rhombohedral space group R3, with unit-cell parameters a = b = 217.48, c = 66.48 A. The protein is also cocrystallized with substrates and diffraction data are collected to 2.7 A resolution

O93623

684168

using sitting-drop vapour-diffusion method at 293 K. Native Tk-glycerol kinase crystals appear after a few days using Wizard I solution No. 25 (0.1 M Tris pH 8.5, 0.2 M MgCl2, 30% PEG 400). Diffraction spots sufficient for structural determination at high resolution are not obtained when a crystal of Tk-glycerol kinase is mounted on a CryoLoop without cryoprotectant, diffraction patterns of the crystal are improved by using Paratone-N as cryoprotectant. Native X-ray diffraction data are collected to 2.4 A resolution using synchrotron radiation at station BL44XU of SPring-8. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = b = 217.48, c = 66.48 A. Assuming the presence of two molecules in the asymmetric unit, the VM value is 2.7 A3Da-1 and the solvent content is 54.1%.

-

677400

-

Thermus aquaticus

-

641327

sitting drop vapor diffusion method, using 30% (w/v) PEG 400 and 100 mM HEPES pH 7.0, at 20°C

5

6 - 7

-

0°C, half-life: 24 h

641295

6 - 9

Mycobacterium sp.

-

30°C, in presence of glycerol, completely stable for 30 min

641287

6 - 8

-

high stability

688443

6.7

Candida mycoderma

-

highest stability

641286

7

7.5

-

25°C, no loss of activity after several h

641287

9.8

-

25°C, half-life: 6.5 min

641287

additional information

-

glycerol affords considerable stabilization at the unfavorable pH values, glycerol kinases from microorganisms most stable at a neutral pH, glycerol kinases from higher organisms most stable in an acidic pH range

641287

20

37

-

2 weeks, stable

641328

50

60

36 entries

65

-

10 min, stable

641328

68

Thermus thermophilus

-

30 min, pH 7.5, 50% activity

641325

70

36 entries

80

-

t1/2: 0.53 min

100

-

30 min, loss of 50% of activity

641319

additional information

(NH4)2SO4 stabilizes

Microsporum gypseum

-

dialysis, against 0.01 M phosphate buffer, at 2°C, pH 6.7, 50% loss of activity without glycerol, stable in presence of 0.01 M glycerol

Candida mycoderma

-

ethanediol stabilizes

Candida mycoderma

-

freezing without glycerol inactivates

-

641308

glycerol affords considerable stabilization at the unfavorable pH values

Mycobacterium sp.

-

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

-

641311

pigeon liver enzyme is sensitive to extreme dilution but can be stabilized by addition of 0.01% bovine serum albumin

Columba sp.

-

the enzyme in crude extracts is stable to freezing and thawing, while more purified preparations are inactivated

susceptible to inactivation by oxidation of sulfhydryl groups

Columba sp.

-

641287

-20°C, 50% glycerol, stable for more than 1 year

-

641308

-20°C, pH 5.0, partially purified enzymes have half-lives of several weeks to months

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

-

641294

4°C, crystallized suspension in 2.2 M ammonium sulfate, stable for several months

Candida mycoderma

-

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

-

13 entries

application of triazine dye affinity chromatography to large-scale purification

-

641306

GSTrap FF column chromatography, gel filtration

-

HiTrapQ HP column, Bio-Scale CHT20-I column, all purification procedures are carried out at 277 K.

-

677400

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; mutant enzyme G230D

-

native and mutant enzyme

-

661122

Ni-NTA agarose column chromatography and Superdex 200 gel filtration