Information on EC 2.7.4.2 - phosphomevalonate kinase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
2.7.4.2
-
RECOMMENDED NAME
GeneOntology No.
phosphomevalonate kinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + (R)-5-phosphomevalonate = ADP + (R)-5-diphosphomevalonate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
isoprene biosynthesis II (engineered)
-
-
Metabolic pathways
-
-
mevalonate pathway I
-
-
Terpenoid backbone biosynthesis
-
-
mevalonate metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:(R)-5-phosphomevalonate phosphotransferase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9026-46-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Madagascar periwinkle
UniProt
Manually annotated by BRENDA team
strain 41
-
-
Manually annotated by BRENDA team
strain 41
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Vitis vinifera x Vitis vinifera
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
-
phosphomevalonate kinase catalyzes the rate-limiting step for biosynthesis of isopentenyl diphosphate from mevalonate
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + (R)-5-diphosphomevalonate
ATP + (R)-5-phosphomevalonate
show the reaction diagram
-
-
-
-
r
ADPbetaS + 5-diphosphomevalonate
ATPbetaS + 5-phosphomevalonate
show the reaction diagram
-
41fold slower kcat than with ADP
-
r
ATP + (R)-5-phosphomevalonate
ADP + (R)-5-diphosphomevalonate
show the reaction diagram
ATP + (R)-5-phosphomevalonate
ADP + 5-diphosphomevalonate
show the reaction diagram
ATP + (R)-mevalonate 5-phosphate
ADP + (R)-mevalonate 5-diphosphate
show the reaction diagram
ATP + (R,S)-5-phosphomevalonate
ADP + (R,S)-5-diphosphomevalonate
show the reaction diagram
ATP + 5-phosphomevalonate
ADP + 5-diphosphomevalonate
show the reaction diagram
CTP + (R,S)-5-phosphomevalonate
CDP + (R,S)-5-diphosphomevalonate
show the reaction diagram
GTP + (R,S)-5-phosphomevalonate
GDP + (R,S)-5-diphosphomevalonate
show the reaction diagram
ITP + 5-phosphomevalonate
IDP + 5-diphosphomevalonate
show the reaction diagram
-
6% of activity with ATP
-
?
TTP + (R,S)-5-phosphomevalonate
TDP + (R,S)-5-diphosphomevalonate
show the reaction diagram
UTP + 5-phosphomevalonate
UDP + 5-diphosphomevalonate
show the reaction diagram
-
13% of activity with ATP
-
?
additional information
?
-
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
ATP + (R)-5-phosphomevalonate
ADP + (R)-5-diphosphomevalonate
show the reaction diagram
ATP + (R)-5-phosphomevalonate
ADP + 5-diphosphomevalonate
show the reaction diagram
ATP + (R)-mevalonate 5-phosphate
ADP + (R)-mevalonate 5-diphosphate
show the reaction diagram
Q15126
the enzyme catalyzes a key step in isoprenoid/sterol biosynthesis
-
-
r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
10 mM cannot replace Mn2+ or Mg2+
Ni2+
-
4.7% of activity with Mg2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-5-diphosphomevalonate
-
-
2,2',2''-(biphenyl-2,4,6-triyltrisulfanediyl)triacetate
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2,2'-[(5,8-dihydroxy-9,10-dioxo-4a,9,9a,10-tetrahydroanthracene-1,4-diyl)diimino]bis(5-methylbenzenesulfonate)
-
-
3-Hydroxy-3-methyl-6-phosphohexanoic acid
-
-
4-hydroxybenzaldehyde
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2.5 mM, 11% inhibition
4-hydroxybenzoic acid
-
2.5 mM, 28% inhibition
4-hydroxyphenylpropionic acid
-
2.5 mM, 46% inhibition
4-[(E)-(2,4-dihydroxyphenyl)diazenyl]-5-methylnaphthalene-2,7-disulfonate
-
-
5,5'-dithiobis(2-nitrobenzoate)
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0.1 mM, almost complete inactivation after 5 min, phosphomevalonate partially protects, inactivation is reverted by 2-mercaptoethanol or dithiothreitol
5-diphosphomevalonate
-
-
AMP-PNP
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competitive dead-end inhibition vs. ATP
Anisic acid
-
2.5 mM, 27% inhibition
Cinnamic acid
-
2.5 mM, 28% inhibition
isoferulic acid
-
2.5 mM, 64% inhibition
luteolin
-
-
m-coumaric acid
-
2.5 mM, 70% inhibition
mevalonate
-
competitive vs. phosphomevalonate, noncompetitive vs. ATP
mevalonate 5-diphosphate
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product inhibition, mutants R111M and R84M show decreased sensitivity compared to the wild-type enzyme
p-coumaric acid
-
1.25 mM, 46% inhibition
phosphomevalonate
-
-
pyridoxal 5'-phosphate
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0.5 mM, 80% inactivation after 30 min, phosphomevalonate protects
pyridoxamine 5'-phosphate
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0.25 mM, 60% inactivation after 20 min
vildagliptin
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treatment reduces the hepatic expression of genes important for cholesterol synthesis and fatty acid oxidation, including phosphomevalonate kinase, acyl-coenzyme dehydrogenase medium chain, mevalonate (diphospho)decarboxylase, and acyl-CoA synthetase in wild-type, but not in dual incretin receptor knock-out mice
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
testosterone
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treatment of meibomian gland stimulates a significant increase in the mRNA levels of mevalonate kinase, phosphomevalonate kinase, mevalonate diphosphate decarboxylase, isopentenyl diphosphate isomerase, geranylgeranyl diphosphate synthase, squalene epoxidase, lanosterol synthase, lanosterol demethylase, and DELTA7-sterol reductase
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.007 - 1.55
(R)-5-diphosphomevalonate
0.012 - 2.04
(R)-5-phosphomevalonate
0.007 - 1.55
(R)-mevalonate 5-diphosphate
0.034 - 2.04
(R)-mevalonate 5-phosphate
0.19
(R,S)-5-phosphomevalonate
-
-
0.042
5-phosphomevalonate
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pH 7.2, 30°C
0.047 - 5.62
ADP
0.38
ADPbetaS
-
pH 7.0, 25°C
0.056 - 5.2
ATP
0.012
diphosphomevalonate
-
pH 7.0, 25°C
0.043 - 1.312
MgATP2-
0.0042 - 0.35
phosphomevalonate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.9
ADP
Streptococcus pneumoniae
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pH 7.0, 25°C
0.095
ADPbetaS
Streptococcus pneumoniae
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pH 7.0, 25°C
3.4
ATP
Streptococcus pneumoniae
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pH 7.0, 25°C
10.2
phosphomevalonate
Sus scrofa
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pH 7.5, 30°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.018 - 1.14
(R)-5-diphosphomevalonate
0.014
5-diphosphomevalonate
-
pH 7.0, 25°C
0.41
ADP
-
pH 7.0, 25°C
0.137
ATP
-
pH 7.0, 25°C
2.48
Cinnamic acid
-
pH 7.4, 37°C
3.85
isoferulic acid
-
pH 7.4, 37°C
0.018 - 1.14
mevalonate 5-diphosphate
2.39
p-coumaric acid
-
pH 7.4, 37°C
0.0077
phosphomevalonate
-
pH 7.0, 25°C
additional information
additional information
-
inhibition kinetics, product inhibition patterns
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
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sharp drop in activity below pH 7.0 and above pH 9.0
7
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8.5
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approx. 50% of maximal activity at pH 6.5 and pH 8.2 respectively
6 - 9.5
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approx. 30% of maximal activity at pH 6.0
6.5 - 8
the enzyme activity drops off below pH 6.5 and above pH 8.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
endogenously expressed human phosphomevalonate kinase and overexpressed human phosphomevalonate kinase
Manually annotated by BRENDA team
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endogenously expressed human phosphomevalonate kinase and overexpressed human phosphomevalonate kinase
Manually annotated by BRENDA team
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from castrated mice. Treatment with androgens may promote cholesterol biosynthesis
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
21000
-
1 * 21000, SDS-PAGE
22900
-
recombinant His-tagged wild-type enzyme, gel filtration
24200
-
1 * 24200, sequence calculation
36200
x * 36200, calculated from sequence
37747
-
x * 37747, MALDI mass spectroscopy
40500
-
2 * 48000, SDS-PAGE, analytical ultracentrifugation, 2 * 40500, amino acid sequence
48000
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2 * 48000, SDS-PAGE, analytical ultracentrifugation, 2 * 40500, amino acid sequence
76000
-
analytical ultracentrifugation
81000
-
calculated from amino acid sequence
128000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
1.8 A resolution. Molecule exhibits a compact alpha/beta structure and shows a sulfate molecule tightly bound to the P-loop. This sulfate ion forms hydrogen bonds with the amino group of amino acid G21 and with the side chain of R141
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NMR-based dynamics and chemical shift experiments of enzyme in complex with MgADP, mevalonate 5-phosphate and the ternary complex. Binding of mevalonate 5-phosphate causes the protein to compress, whereas subsequent binding of MgADP opens the structure. Mevalonate 5-phosphate causes movement around a hinge region to permit domain closure. Amino acids H55 and R93 may act as hinge residues, D163 may be a hinge residue for the lid region. Binding of ATP or ADP causes similar conformational changes. The first nine residues of the N-terminus are highly disordered
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purified recombinant His6-tagged enzyme, mixing of 0.002 ml of 10 mg/mL protein in 100 mM (NH4)2SO4, 20 mM HEPES, pH 7.6, with 0.002 ml reservoir solution containing 15% v/v pentaerythritol ethoxylate, 100 mM HEPES, pH 7.6, 15% v/v MPD, 15°C, 2-3 days, X-ray diffraction structure determination and analysis at 1.76 A resolution, SAD method
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enzyme in a ternary complex with phosphomevalonate, AMPPNP, and Mg2+, by sitting drop method, mixing 0.002 ml of 12 mg/ml PMK in 25 mM HEPES/K+, pH 7.5, 0.25 mM phosphomevalonate, 8 mM AMPPNP, 10 mM MgCl2, with 0.002 ml of 36% w/v PEG 4000, and 100 mM MES/Na+, pH 6.0, X-ray diffraction structure determination and analysis at 1.9 A resolution, molecular replacement with EPMR
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hanging-drop vapor diffusion at 20°C against a reservoir containing 100 mM HEPES pH 7.5, 800 mM NaH2PO4, 8000 mM KH2PO4 and 30 mM unbuffered ATP, crystals diffract to 2.4 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7.5
-
unstable below pH 6.0 and above pH 7.5
645176
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
70% loss of activity after 30 min
45
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complete loss of activity after 30 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
sulfhydryl reagents are not essential to protect the activity of phosphomevalonate kinase
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
very unstable in absence of thiol compounds
-
645174
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10°C, 1 month, no loss of activity
-
-20°C, 10 mM Tris or phosphate buffer, pH 7.5, 50% glycerol, 10 mM 2-mercaptoethanol, 60 days, no loss of activity
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-20°C, 10 mM Tris-HCl, pH 7.5, 1 mM dithiothreitol, 50% glycerol, 15 months, 20% loss of acctivity
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-20°C, 50% glycerol
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4°C, 10 mM 2-mercaptoethanol, 3 months, no loss of activity
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4°C, 20 days, 99% loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, DEAE-cellulose, BioGel P-150, hydroxylapatite, Blue Dextran-Sepharose
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ammonium sulfate, ethanol, phosphate gel, DEAE-cellulose
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native enzyme from liver
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Ni-NTA resin column chromatography
Ni-Sepharose column chromatography
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Q Sepharose, Phenyl Sepharose, Sephacryl S200, Mono Q, gel filtration, Shodex KW803
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recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
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recombinant protein
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Se-Met fusion protein, glutathione and Sepharose Q resins
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Sephadex G-200
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in CV-1 cells; expression in human embryonic kidney (HEK-293) Flp-In and CV1 cells
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expressed in Escherichia coli BL21 (DE3) Rosetta cells
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expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli DH10B cells
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expression in Escherichia coli
expression in Escherichia coli BL21(DE3)
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expression of phosphomevalonate kinase-green fluorescence fusion protein in CHO cells and fibroblasts
expression of the C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
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gene PMVK, DNA and amino acid sequence determination and analysis, functional expression of soluble His-tagged wild-type enzyme and of His-tagged mutants in Escherichia coli strains JM109 and BL21(DE3)
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gene PMVK, expression of His-tagged wild-type enzyme and mutants in Escherichia coli strain BL21(DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D23N
-
site-directed mutagenesis, the mutant shows highly reduced activity in both forward and reverse reactions compared to the wild-type enzyme
K17M
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site-directed mutagenesis, the mutant shows reduced activity in both forward and reverse reactions compared to the wild-type enzyme
K19M
-
site-directed mutagenesis, the mutant shows highly reduced activity in both forward and reverse reactions compared to the wild-type enzyme
K22M
-
site-directed mutagenesis, the mutant shows a 10000fold reduced activity in both forward and reverse reactions compared to the wild-type enzyme, almost inactive mutant
K48M
-
mutant exhibits diminished Vmax values in both reaction directions with only slight Km perturbations; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
K69M
-
mutant exhibits diminished Vmax values in both reaction directions with only slight Km perturbations
R110M
-
no catalytic activity; site-directed mutagenesis, the mutant shows altered kinetics and highly reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R111M
-
site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme; substantially inflated Km values for mevalonate 5-phosphate and mevalonate 5-diphosphate
R130M
-
mutant exhibits slight changes in Vmax values in both reaction directions with slight Km perturbations; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R138M
-
mutant exhibits slight changes in Vmax values in both reaction directions with slight Km perturbations; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R141M
-
50fold increase in Km value for ATP, 120fold increase for ADP; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R18Q
-
site-directed mutagenesis, the mutant shows highly reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R73M
-
mutant exhibits diminished Vmax values in both reaction directions with only slight Km perturbations; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R84M
-
50- and 33fold increase in Km value for mevalonate 5-phosphate and mevalonate 5-diphosphate, respectively; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
R93M
-
mutant exhibits slight changes in Vmax values in both reaction directions with slight Km perturbations; site-directed mutagenesis, the mutant shows altered kinetics and reduced activity in both forward and reverse reactions compared to the wild-type enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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