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 , and Eric Weitz

Activity

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Organisms

Homo sapiens

Communities

Annotations

Disease Ontology

pernicious anemia

Pathway Ontology

cobalamin metabolic pathway

Participants

Label 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
F2-Isoprostane Metabolite wikidata:Q33659470
Thromboxane B2 Metabolite hmdb:HMDB0003252
a-Tocopherol Metabolite hmdb:HMDB0001893 Vitamin E
8-Isoprostaglandin F2a Metabolite hmdb:HMDB0005083
PGE2 Metabolite hmdb:HMDB0001220 Prostaglandin E2
PGE1 Metabolite hmdb:HMDB0001442 Prostaglandin E1
PGF2a Metabolite hmdb:HMDB0001139 Prostaglandin F2a
Thromboxane B2 Metabolite hmdb:HMDB0003252
PGE1 Metabolite hmdb:HMDB0001442 Prostaglandin E1
a-Tocopherol Metabolite hmdb:HMDB0001893 Vitamin E
Thromboxane A2 Metabolite hmdb:HMDB0001452
NADH Metabolite hmdb:HMDB0001487 Reduced nicotinamide adenine diphosphate
NADP+ Metabolite hmdb:HMDB0000217 Nicotinamide adenine dinucleotide phosphate-Oxidized
NADP+ Metabolite hmdb:HMDB0000217 Nicotinamide adenine dinucleotide phosphate-Oxidized
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 anhydride
A breakdown product of creatine phosphate in muscle
5-methyl-THF Metabolite hmdb:HMDB0001396 5-methyltetrahydrofolate
Predominant food folate
Creatinine Metabolite hmdb:HMDB0000562 Creatine anhydride
A breakdown product of creatine phosphate in muscle
5-methyl-THF Metabolite hmdb:HMDB0001396 5-methyltetrahydrofolate
Predominant food folate
THF Metabolite hmdb:HMDB0001846 Tetrahydrofolic acid
NADPH Metabolite hmdb:HMDB0000221 Nicotinamide adenine dinucleotide phosphate-Reduced
NADPH Metabolite hmdb:HMDB0000221 Nicotinamide adenine dinucleotide phosphate-Reduced
NADPH Metabolite hmdb:HMDB0000221 Nicotinamide adenine dinucleotide phosphate-Reduced
NAD Metabolite hmdb:HMDB0000902 Nicotinamide adenine dinucleotide
Homocysteine Metabolite hmdb:HMDB0000742
Homocysteine Metabolite hmdb:HMDB0000742
Pyridoxal 5'-phosphate Metabolite hmdb:HMDB0001491 Vitamin B6
Pyridoxal 5'-phosphate Metabolite hmdb:HMDB0001491 Vitamin B6
Serine Metabolite hmdb:HMDB0000187
Serine Metabolite hmdb:HMDB0000187
LDL Metabolite chebi:39026 low-density lipoprotein
VLDL-TAG Metabolite chebi:47776 very-low-density lipoprotein-triglyceride
Triglyceride transport
HDL-C Metabolite chebi:47775 high-density lipoprotein cholesterol
Cholesterol transport
VLDL Metabolite chebi:39027 very-low-density lipoprotein
LDL Metabolite chebi:39026 low-density lipoprotein
HDL Metabolite chebi:39025 high-density lipoprotein
LDL/APOB Metabolite chebi:39026 low-density lipoprotein
LDL particle contains 1 molecule of apo B
VLDL/APOB Metabolite chebi:39027 very-low-density lipoprotein
The 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 Triglyceride
Triacylglycerol
HDL-C Metabolite chebi:47775 high-density lipoprotein cholesterol
Cholesterol transport
VLDL-TAG Metabolite chebi:47776 very-low-density lipoprotein-triglyceride
Triglyceride transport
oxLDL Metabolite chebi:60151 oxidized low-density lipoprotein
LDL-C Metabolite chebi:47774 low-density lipoprotein cholesterol
HDL Metabolite chebi:39025 high-density lipoprotein
TAG Metabolite chebi:17855 Triglyceride
Triacylglycerol
HDL/SAA Metabolite chebi:39025 high-density lipoprotein
SAA circulates in plasma as a constituent of high density lipoproteins (HDL).
VLDL Metabolite chebi:39027 very-low-density lipoprotein
Cholesterol Metabolite hmdb:HMDB0000067
HDL/APOA1 Metabolite chebi:39025 high-density lipoprotein
ApoA-I is present on the majority of HDL particles and constitutes aprox 70% of the apolipoprotein content of HDL particles
Adenosylcobalamin Metabolite hmdb:HMDB0002086
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
8-OHdG Metabolite hmdb:HMDB0003333 8-Hydroxy-deoxyguanosine
Methylcob(III)alamin Metabolite hmdb:HMDB0002274
Chlorine Metabolite hmdb:HMDB0000492
vitamin D Metabolite chebi:27300
vitamin D Metabolite chebi:27300
Chlorine Metabolite hmdb:HMDB0000492
Cystathionine Metabolite hmdb:HMDB0000099
Zinc Metabolite hmdb:HMDB0015532
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 oxide
Nitrous 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-Adenosylhomocysteine Metabolite hmdb:HMDB0000939
S-Adenosylmethionine Metabolite hmdb:HMDB0001185
Succinyl-CoA Metabolite hmdb:HMDB0001022
Methylmalonic acid Metabolite hmdb:HMDB0000202 Methylmalonate
Cbl/TC Metabolite hmdb:HMDB0002174 Cobalamin Transcobalamin complex
Methylmalonic acid Metabolite hmdb:HMDB0000202 Methylmalonate
L-Methylmalonyl-CoA Metabolite hmdb:HMDB0001269
Cbl/IF Metabolite hmdb:HMDB0002174 Cobalamin Intrinsic factor complex
Cbl/HC Metabolite hmdb:HMDB0002174 Cobalamin haptocorrin complex
Methionine Metabolite hmdb:HMDB0000696
D-Methylmalonyl-CoA Metabolite hmdb:HMDB0001269
Cbl/TC Metabolite hmdb:HMDB0002174 Cobalamin Transcobalamin complex
Holotranscobalamin
S-Adenosylmethionine Metabolite hmdb:HMDB0001185
Nitrotyrosine Metabolite hmdb:HMDB0001904
ONOO-ONOOH Metabolite hmdb:HMDB0002179 Peroxynitrite
Fructosamine Metabolite hmdb:HMDB0002030
Fructosamine Metabolite hmdb:HMDB0002030
Glucose Metabolite hmdb:HMDB0000122
Glucose Metabolite hmdb:HMDB0000122
Ascorbic acid Metabolite chebi:29073 Vitamin C
Ascorbic acid Metabolite chebi:29073 Vitamin C
Ascorbic acid Metabolite chebi:29073 Vitamin C
MCP1 GeneProduct ncbigene:6347 Monocyte Chemotactic Protein 1
CCL2
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
MCP1 GeneProduct ncbigene:6347 Monocyte Chemotactic Protein 1
CCL2
RELA GeneProduct ncbigene:5970 nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, p65
TCN2* GeneProduct ncbigene:6948 transcobalamin II; macrocytic anemia
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 1.16.1.4
cob(II)alamin reductase
MMAB Protein ncbigene:326625 EC 2.5.1.17
methylmalonic aciduria (cobalamin deficiency) cblB type
Also known as ATR
MAT Protein ncbigene:4143 EC 2.5.1.6
Methionine adenosyltransferase
MTR* Protein ncbigene:4548 EC 2.1.1.13
5-methyltetrahydrofolate-homocysteine methyltransferase
Also known as MS
MCEE Protein ncbigene:84693 EC 5.1.99.1
methylmalonyl CoA epimerase
MSR* Protein ncbigene:4552 EC 1.16.1.8
5-methyltetrahydrofolate-homocysteine methyltransferase reductase
MUT Protein ncbigene:4594 EC 5.4.99.2
methylmalonyl Coenzyme A mutase
Also known as MCM
SHMT Protein ncbigene:6472 EC 2.1.2.1
Serine hydroxymethyltransferase
CBS Protein ncbigene:875 EC 4.2.1.22
cystathionine-beta-synthase
MPO Protein ncbigene:4353 EC 1.11.1.7
Myeloperoxidase
PAI-1 Protein ncbigene:5054 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
tPA Protein ncbigene:5327 EC 3.4.21.68
plasminogen activator, tissue
PAI-1 Protein ncbigene:5054 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
tPA Protein ncbigene:5327 EC 3.4.21.68
plasminogen activator, tissue
PLG Protein ncbigene:5340 EC 3.4.21.7
Plasminogen
Thrombin Protein ncbigene:2147 EC 3.4.21.5
coagulation factor II (thrombin)
Thrombin Protein ncbigene:2147 EC 3.4.21.5
coagulation factor II (thrombin)
Factor VII Protein ncbigene:2155 EC 3.4.21.21
coagulation factor VII (serum prothrombin conversion accelerator)
Factor VII Protein ncbigene:2155 EC 3.4.21.21
coagulation factor VII (serum prothrombin conversion accelerator)
PLG Protein ncbigene:5340 EC 3.4.21.7
Plasminogen
SOD3 Protein ncbigene:6649 EC 1.15.1.1
superoxide dismutase 3, extracellular
SOD3 Protein ncbigene:6649 EC 1.15.1.1
superoxide dismutase 3, extracellular
CTH Protein ncbigene:1491 EC 4.4.1.1
cystathionase
MTHFR* Protein ncbigene:4524 EC 1.5.1.20
5,10-methylenetetrahydrofolate reductase
Homozygous 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 1.15.1.1
superoxide dismutase 1, soluble
ACT Protein ncbigene:12 alpha-1-antichymotrypsin
serpin 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
APOB Protein ncbigene:338 apolipoprotein B
ACT Protein ncbigene:12 alpha-1-antichymotrypsin
serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3
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
APOA1 Protein ncbigene:335 apolipoprotein A-I
SAA2 Protein ncbigene:6289 serum amyloid A2
SOD2 Protein ncbigene:6648 EC 1.15.1.1
superoxide 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 hemoglobin
http://en.wikipedia.org/wiki/Glycated_hemoglobin
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
INS Protein ncbigene:3630 Insulin
ALB Protein ncbigene:213 albumin
RANTES Protein ncbigene:6352 CCL5
chemokine (C-C motif) ligand 5
IL6 Protein ncbigene:3569 interleukin 6 (interferon, beta 2)
HBA1 Protein ncbigene:3039 hemoglobin, alpha 1
D-dimer Protein wikidata:Q2162109 http://en.wikipedia.org/wiki/Fibrin_degradation_product
sICAM-1 Protein ncbigene:3383 soluble intercellular adhesion molecule 1
IL1B Protein ncbigene:3553 interleukin 1, beta
IL10 Protein ncbigene:3458 interferon, gamma
TNFa Protein ncbigene:7124 tumor necrosis factor (TNF superfamily, member 2)
HBB Protein ncbigene:3043 hemoglobin, beta
Fibrin Protein wikidata:Q27205
CRP Protein ncbigene:1401 C-reactive protein, pentraxin-related
RANTES Protein ncbigene:6352 CCL5
chemokine (C-C motif) ligand 5
HbA1c Protein wikidata:Q311213 Glycated hemoglobin
http://en.wikipedia.org/wiki/Glycated_hemoglobin

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