Vitamin B12 metabolism (WP1533)
Homo sapiens
Vitamin B12 is a water soluble, organic compound and essential nutrient involved in the everyday functioning of the nervous system and the brain. Vitamin B12 is involved in the preservation and regeneration of the myelin shealth - the protective fatty layer that acts as an insulator in nerve axons. Animals store vitamin B12 in liver and muscle and therefore eggs, milk, meat, liver are sources of the vitamin. Problems in metabolism of vitamin B12 lead to "persistent" lack of energy to perform every day tasks. The genes and pathways highlighted above describe several routes through which genes and metabolites involved in B12 metabolism are interconnected. Central B12 metabolism nodes include folate metabolism and the synthesis of the citric acid cycle intermediates and succinyl-CoA, cyanocobalamin into methylcobalamin conversion, tyrosine nitration and riboflavin pathways. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP1533 CPTAC Assay Portal].
Authors
Damariz Rivero , Kristina Hanspers , Alex Pico , Andra Waagmeester , Egon Willighagen , Martina Summer-Kutmon , Asios Olia , Friederike Ehrhart , Denise Slenter , Eric Weitz , and Aishwarya IyerActivity
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Cited In
- Identifying Drug-Induced Liver Injury Associated With Inflammation-Drug and Drug-Drug Interactions in Pharmacologic Treatments for COVID-19 by Bioinformatics and System Biology Analyses: The Role of Pregnane X Receptor (2022).
- Target and drug predictions for SARS-CoV-2 infection in hepatocellular carcinoma patients (2022).
- Heterogeneity of Lipid and Protein Cartilage Profiles Associated with Human Osteoarthritis with or without Type 2 Diabetes Mellitus (2021).
- Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients (2021).
- Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients (2020).
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Organisms
Homo sapiensCommunities
Annotations
Pathway Ontology
cobalamin metabolic pathwayDisease Ontology
pernicious anemiaLabel | Type | Compact URI | Comment |
---|---|---|---|
PGE2 | Metabolite | hmdb:HMDB0001220 | Prostaglandin E2 |
Thromboxane B2 | Metabolite | hmdb:HMDB0003252 | |
PGF2a | Metabolite | hmdb:HMDB0001139 | Prostaglandin F2a |
8-Isoprostaglandin F2a | Metabolite | hmdb:HMDB0005083 | |
F2-Isoprostane | Metabolite | wikidata:Q33659470 | |
a-Tocopherol | Metabolite | hmdb:HMDB0001893 | Vitamin E |
PGE1 | Metabolite | hmdb:HMDB0001442 | Prostaglandin E1 |
Thromboxane A2 | Metabolite | hmdb:HMDB0001452 | |
NADH | Metabolite | hmdb:HMDB0001487 | Reduced nicotinamide adenine diphosphate |
NADP+ | Metabolite | hmdb:HMDB0000217 | Nicotinamide adenine dinucleotide phosphate-Oxidized |
Cysteine | Metabolite | hmdb:HMDB0000574 | |
H2O2 | Metabolite | hmdb:HMDB0003125 | Hydrogen peroxide |
5,10-Methylene-THF | Metabolite | hmdb:HMDB0001533 | 5,10-Methylenetetrahydrofolate |
Creatinine | Metabolite | hmdb:HMDB0000562 | Creatine anhydrideA breakdown product of creatine phosphate in muscle |
5-methyl-THF | Metabolite | hmdb:HMDB0001396 | 5-methyltetrahydrofolatePredominant food folate |
THF | Metabolite | hmdb:HMDB0001846 | Tetrahydrofolic acid |
NADPH | Metabolite | hmdb:HMDB0000221 | Nicotinamide adenine dinucleotide phosphate-Reduced |
NAD | Metabolite | hmdb:HMDB0000902 | Nicotinamide adenine dinucleotide |
Homocysteine | Metabolite | hmdb:HMDB0000742 | |
Pyridoxal 5'-phosphate | Metabolite | hmdb:HMDB0001491 | Vitamin B6 |
Serine | Metabolite | hmdb:HMDB0000187 | |
LDL | Metabolite | chebi:39026 | low-density lipoprotein |
VLDL-TAG | Metabolite | chebi:47776 | very-low-density lipoprotein-triglycerideTriglyceride transport |
HDL-C | Metabolite | chebi:47775 | high-density lipoprotein cholesterolCholesterol transport |
VLDL | Metabolite | chebi:39027 | very-low-density lipoprotein |
HDL | Metabolite | chebi:39025 | high-density lipoprotein |
LDL/APOB | Metabolite | chebi:39026 | low-density lipoproteinLDL particle contains 1 molecule of apo B |
VLDL/APOB | Metabolite | chebi:39027 | very-low-density lipoproteinThe VLDL is produced in the liver, contains one molecule of apoB100 |
oxLDL | Metabolite | chebi:60151 | oxidized low-density lipoprotein |
LDL-C | Metabolite | chebi:47774 | low-density lipoprotein cholesterol |
Cholesterol | Metabolite | hmdb:HMDB0000067 | |
TAG | Metabolite | chebi:17855 | TriglycerideTriacylglycerol |
LDL-C | Metabolite | chebi:47774 | low-density lipoprotein cholesterol |
HDL/SAA | Metabolite | chebi:39025 | high-density lipoproteinSAA circulates in plasma as a constituent of high density lipoproteins (HDL). |
HDL/APOA1 | Metabolite | chebi:39025 | high-density lipoproteinApoA-I is present on the majority of HDL particles and constitutes aprox 70% of the apolipoprotein content of HDL particles |
Adenosylcobalamin | Metabolite | hmdb:HMDB0002086 | |
Methylcob(III)alamin | Metabolite | hmdb:HMDB0002274 | |
Vitamin B12/Cobalamin | Metabolite | hmdb:HMDB0002174 | |
Cob(II)alamin | Metabolite | hmdb:HMDB0006316 | oxidized cobalamin |
Vitamin B12 / cobalamin | Metabolite | hmdb:HMDB0002174 | |
Cob(I)alamin | Metabolite | hmdb:HMDB0003429 | Reduced cobalamin |
FAD | Metabolite | hmdb:HMDB0001248 | Flavin adenine dinucleotide |
8-OHdG | Metabolite | hmdb:HMDB0003333 | 8-Hydroxy-deoxyguanosine |
Chlorine | Metabolite | hmdb:HMDB0000492 | |
vitamin D | Metabolite | chebi:27300 | |
Cystathionine | Metabolite | hmdb:HMDB0000099 | |
Zinc | Metabolite | hmdb:HMDB0015532 | |
NO | Metabolite | hmdb:HMDB0003378 | Nitric oxide |
NO3- | Metabolite | hmdb:HMDB0002878 | Nitrate |
NO2 | Metabolite | chebi:33101 | Nitrogen dioxide |
O3 | Metabolite | chebi:25812 | ozone |
HOCl | Metabolite | hmdb:HMDB0001050 | Hypochlorite |
HNO2 | Metabolite | chebi:25567 | Nitrous acid |
N2O | Metabolite | chebi:17045 | Dinitrogen oxideNitrous oxide |
Fibrin | Metabolite | wikidata:Q27205 | |
Riboflavin | Metabolite | hmdb:HMDB0000244 | Also known as vitamin B2 |
Riboflavin | Metabolite | hmdb:HMDB0000244 | |
O2 | Metabolite | hmdb:HMDB0002168 | Superoxide |
S-Adenosylhomocysteine | Metabolite | hmdb:HMDB0000939 | |
Methionine | Metabolite | hmdb:HMDB0000696 | |
S-Adenosylmethionine | Metabolite | hmdb:HMDB0001185 | |
Succinyl-CoA | Metabolite | hmdb:HMDB0001022 | |
Methylmalonic acid | Metabolite | hmdb:HMDB0000202 | Methylmalonate |
Cbl/TC | Metabolite | hmdb:HMDB0002174 | Cobalamin Transcobalamin complex |
L-Methylmalonyl-CoA | Metabolite | hmdb:HMDB0001269 | |
Cbl/IF | Metabolite | hmdb:HMDB0002174 | Cobalamin Intrinsic factor complex |
Cbl/HC | Metabolite | hmdb:HMDB0002174 | Cobalamin haptocorrin complex |
D-Methylmalonyl-CoA | Metabolite | hmdb:HMDB0001269 | |
Cbl/TC | Metabolite | hmdb:HMDB0002174 | Cobalamin Transcobalamin complexHolotranscobalamin |
Nitrotyrosine | Metabolite | hmdb:HMDB0001904 | |
ONOO-ONOOH | Metabolite | hmdb:HMDB0002179 | Peroxynitrite |
Fructosamine | Metabolite | hmdb:HMDB0002030 | |
Glucose | Metabolite | hmdb:HMDB0000122 | |
Ascorbic acid | Metabolite | chebi:29073 | Vitamin C |
MCP1 | GeneProduct | ncbigene:6347 | Monocyte Chemotactic Protein 1CCL2 |
NFKB2 | GeneProduct | ncbigene:4791 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 |
IF* | GeneProduct | ncbigene:2694 | gastric intrinsic factor (vitamin B synthesis)Also known as GIF |
TCN2* | GeneProduct | ncbigene:6948 | transcobalamin II; macrocytic anemia |
RELA | GeneProduct | ncbigene:5970 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, p65 |
HC | GeneProduct | ncbigene:6947 | Haptocorrin transcobalamin I (vitamin B12 binding protein, R binder family) |
Megalin | GeneProduct | ncbigene:4036 | Low density lipoprotein receptor-related protein 2 |
CUBN | GeneProduct | ncbigene:8029 | cubilin (intrinsic factor-cobalamin receptor) |
NFKB1 | GeneProduct | ncbigene:4790 | nuclear factor NF-kappa-B p50 subunit |
MM-CoA-H | Protein | eccode:3.1.2.17 | EC 3.1.2.17(S)-methylmalonyl-CoA hydrolase |
CBR | Protein | eccode:1.16.1.4 | EC 1.16.1.4cob(II)alamin reductase |
MMAB | Protein | ncbigene:326625 | EC 2.5.1.17methylmalonic aciduria (cobalamin deficiency) cblB typeAlso known as ATR |
MAT | Protein | ncbigene:4143 | EC 2.5.1.6Methionine adenosyltransferase |
MTR* | Protein | ncbigene:4548 | EC 2.1.1.135-methyltetrahydrofolate-homocysteine methyltransferaseAlso known as MS |
MCEE | Protein | ncbigene:84693 | EC 5.1.99.1methylmalonyl CoA epimerase |
MSR* | Protein | ncbigene:4552 | EC 1.16.1.85-methyltetrahydrofolate-homocysteine methyltransferase reductase |
MUT | Protein | ncbigene:4594 | EC 5.4.99.2methylmalonyl Coenzyme A mutaseAlso known as MCM |
SHMT | Protein | ncbigene:6472 | EC 2.1.2.1Serine hydroxymethyltransferase |
CBS | Protein | ncbigene:875 | EC 4.2.1.22cystathionine-beta-synthase |
MPO | Protein | ncbigene:4353 | EC 1.11.1.7Myeloperoxidase |
PAI-1 | Protein | ncbigene:5054 | Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 |
tPA | Protein | ncbigene:5327 | EC 3.4.21.68plasminogen activator, tissue |
PLG | Protein | ncbigene:5340 | EC 3.4.21.7Plasminogen |
Thrombin | Protein | ncbigene:2147 | EC 3.4.21.5coagulation factor II (thrombin) |
Factor VII | Protein | ncbigene:2155 | EC 3.4.21.21coagulation factor VII (serum prothrombin conversion accelerator) |
SOD3 | Protein | ncbigene:6649 | EC 1.15.1.1superoxide dismutase 3, extracellular |
CTH | Protein | ncbigene:1491 | EC 4.4.1.1cystathionase |
MTHFR* | Protein | ncbigene:4524 | EC 1.5.1.205,10-methylenetetrahydrofolate reductaseHomozygous of (MTHFR) 677C-T variant may have enzyme activities up to 50% lower than those without the polymorphism increasing the risk of hyperhomocysteinemia |
SOD1 | Protein | ncbigene:6647 | EC 1.15.1.1superoxide dismutase 1, soluble |
ACT | Protein | ncbigene:12 | alpha-1-antichymotrypsinserpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 |
LDLR | Protein | ncbigene:3949 | low density lipoprotein receptor |
APOB | Protein | ncbigene:338 | apolipoprotein B |
SRB1 | Protein | ncbigene:949 | scavenger receptor class B, member 1 |
ABCA1 | Protein | ncbigene:19 | ATP-binding cassette, sub-family A (ABC1), member 1 |
SAA4 | Protein | ncbigene:6291 | serum amyloid A4, constitutive |
SAA3 | Protein | ncbigene:6290 | serum amyloid A3 pseudogene |
APOA1 | Protein | ncbigene:335 | apolipoprotein A-I |
SAA1 | Protein | ncbigene:6288 | serum amyloid A1 |
APOE | Protein | ncbigene:348 | apolipoprotein A-I |
APOA1-NO2Tyr | Protein | ncbigene:335 | Nitrotyrosinated apolipoprotein A-I |
SAA2 | Protein | ncbigene:6289 | serum amyloid A2 |
SOD2 | Protein | ncbigene:6648 | EC 1.15.1.1superoxide dismutase 2, mitochondrial |
D-dimer | Protein | wikidata:Q2162109 | http://en.wikipedia.org/wiki/Fibrin_degradation_product |
TNFa | Protein | ncbigene:7124 | tumor necrosis factor (TNF superfamily, member 2) |
HbA1c | Protein | wikidata:Q311213 | Glycated hemoglobinhttp://en.wikipedia.org/wiki/Glycated_hemoglobin |
Fibrinogen | Protein | wikidata:Q381899 | |
IL1B | Protein | ncbigene:3553 | interleukin 1, beta |
INSR | Protein | ncbigene:3643 | Insulin receptor |
IL6 | Protein | ncbigene:3569 | interleukin 6 (interferon, beta 2) |
IL10 | Protein | ncbigene:3458 | interferon, gamma |
ALB | Protein | ncbigene:213 | albumin |
INS | Protein | ncbigene:3630 | Insulin |
RANTES | Protein | ncbigene:6352 | CCL5 chemokine (C-C motif) ligand 5 |
HBA1 | Protein | ncbigene:3039 | hemoglobin, alpha 1 |
sICAM-1 | Protein | ncbigene:3383 | soluble intercellular adhesion molecule 1 |
HBB | Protein | ncbigene:3043 | hemoglobin, beta |
Fibrin | Protein | wikidata:Q27205 | |
CRP | Protein | ncbigene:1401 | C-reactive protein, pentraxin-related |
RANTES | Protein | ncbigene:6352 | CCL5chemokine (C-C motif) ligand 5 |
FGA | Protein | ncbigene:2243 | |
FGB | Protein | ncbigene:2244 | |
FGG | Protein | ncbigene:2266 |
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