Vitamin B12 metabolism (Homo sapiens)

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23, 88, 26429, 75, 179, 180, 201...6042, 47, 73, 75109, 230InhibitionSelenoproteinsCofactorsReactionNitrogen CompundsCleavageCofactor conversionProtein*Necessary stimulationProcess or metabolism involved in Se PathwayFrom intracellular part to the plasmaMetabolitesis composed ofConversionLEGENDEnzymesBindingProtein with polymorphismStimulationMicronutrientsBiomarker forOther proteinsOverarching processNegative EffectSelenium statusTranscription factorCatalysisIntracellularPlasmaIF*8-Isoprostaglandin F2aTCN2*PGE2MegalinF2-IsoprostaneCUBNa-Tocopherol8-Isoprostaglandin F2aMCP1TCN2*NFKB2Thromboxane B2Thromboxane B2PGE1Lipoprotein metabolismPGE2a-TocopherolMCP1Prostaglandin metabolismThromboxane A2PGF2aNFKB1F2-IsoprostanePGF2aThromboxane B2RELADNA OxidationLipid peroxidationProtein tyrosine nitrationHCPGE125377, 81, 104, 130, 141...212, 22626, 24159, 139, 144139, 222139, 22226, 237, 24178, 13836, 1452277, 81, 104, 130, 141...241, 81, 104, 130, 200...8, 12, 82, 114, 270...296245, 81, 104, 1301441448, 12, 82, 114, 270...14436, 14581, 104, 13062, 139, 164121, 130, 20062, 139, 164MCEEMM-CoA-HMTR*SHMTCBRMUTMMABMSR*MAT814, 274245184, 265130, 14255184, 22081, 126, 224, 276, 280CBS194NADP+NADP+NADP+NADHMPO73, 168, 258CysteinePLGThrombinFactor VIIPAI-1Factor VIIPAI-1ThrombintPAPLGtPA39, 22839, 9430039, 9430030030039, 228300300H2O25,10-Methylene-THF111, 274CreatinineCreatinine5-methyl-THF5-methyl-THF109, 111, 163, 230, 264...109, 111, 163, 230, 264...160, 281160, 281SOD3SOD3CTHTHF111NADNADPHNADPHNADPHMTHFR*111, 276HomocysteineHomocysteine26, 57, 66, 75, 128...26, 57, 66, 75, 128...SOD1Pyridoxal 5'-phosphatePyridoxal 5'-phosphate145, 163, 264145, 163, 264SerineSerine4, 2744, 274CholesterolHDL/SAAHDL/APOA1SRB1APOEABCA1APOA1LDLRSAA4LDL-CoxLDLLDL/APOBHDLAPOBTAGSAA3ACTSAA1VLDLHDL-CSAA2LDL-CoxLDLHDL-CAPOBVLDL-TAGAPOA1HDLTAGCholesterolVLDL-TAGAPOA1-NO2TyrLDLVLDLACTVLDL/APOBLDL18, 252137, 29918, 4118, 17113718, 171132, 18918137, 299189, 299132, 156114, 226, 241137132, 15618107, 137181884, 190, 233288114, 226, 24184, 190, 2331813718, 17118, 17113718114, 226, 241107, 13718, 41, 241252190, 23318114, 226, 24118, 171, 252137Cob(II)alaminMethylcob(III)alamin8-OHdGVitamin B12/CobalaminAdenosylcobalaminCob(I)alaminAdenosylcobalaminMethylcob(III)alaminVitamin B12/Cobalamin8-OHdGFAD81, 109, 184, 23066, 79, 81, 84, 104...81, 14266, 81, 84, 104, 130...25381, 18481, 109, 184, 23081, 14225350, 81, 184Chlorinevitamin DChlorinevitamin D8484CystathionineSOD2ZincZincN2ONO2O3NONO3-HNO2HOCl126, 22457, 126, 168, 258RANTESHBBsICAM-1FibrinFibrinogenINSHbA1cIL1BIL1BD-dimerD-dimerIL10CRPTNFaIL10HBA1FibrinogenINSRRANTESIL6FibrinIL6ALBINSALBHbA1cTNFa146, 2009, 86, 114, 138, 264...2923, 88, 264862943, 75, 8623, 7562, 75, 180237, 24443, 123, 211146, 20094, 30075, 18043, 123, 211237, 24435, 43196140, 300196140, 30019643, 62, 75, 79, 8623, 75, 273, 28294, 300196RiboflavinRiboflavin84, 14384, 143O2Cbl/IFL-Methylmalonyl-CoACbl/TC S-AdenosylhomocysteineCbl/HC Succinyl-CoACbl/TC S-Adenosylmethionine S-Adenosylmethionine S-AdenosylhomocysteineMethionineMethionineD-Methylmalonyl-CoA Methylmalonic acid Methylmalonic acid130, 14233, 11181, 104, 130142130, 14281, 104, 130, 160111, 262, 28081, 104, 13055, 111, 184, 186130, 14255, 111, 184, 186111, 262, 28081, 104, 13066, 14233, 111ONOO-ONOOHNitrotyrosine296GlucoseGlucoseFructosamineFructosamine123, 196123, 196146146Ascorbic acidAscorbic acidAscorbic acid82, 166, 27082, 166, 27082, 166, 270FGAFGBFGG


Description

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 CPTAC Assay Portal.

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Bibliography

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History

View all...
CompareRevisionActionTimeUserComment
129486view10:04, 30 April 2024EgonwTagged many interaction as 'mim-translocation' for a comment "From intracellular part to the plasma"
129484view09:44, 30 April 2024EgonwAdded a few identifiers
121695view03:29, 26 February 2022EweitzUse official gene symbol
120920view06:32, 31 January 2022EgonwReplaced an old HMDB identifier with the current one
116401view00:04, 7 May 2021EweitzModified title
107121view14:19, 17 September 2019MaintBotChEBI identifier normalization
106696view13:04, 17 September 2019MaintBotHMDB identifier normalization
105852view23:16, 15 August 2019KhanspersModified description
105138view15:07, 10 July 2019DeSlConnected unconnected lines.
105137view15:00, 10 July 2019DeSlUpdated Fibrinogen as complex with 3 subunits, changed fibrin datanode type from protein to metabolite.
101942view06:31, 19 November 2018EgonwReplaced Wikipedia with Wikidata identifiers.
98243view14:14, 14 August 2018EgonwReplace a PubChem SID with a Wikidata ID (which has more links out).
97371view18:33, 11 May 2018AlexanderPicofixed legend for metabolites
97370view18:31, 11 May 2018AlexanderPicodistinguished cofactor color
97369view18:30, 11 May 2018AlexanderPicodistinguished cofactor color
97368view18:27, 11 May 2018AlexanderPicoadditional color fixes
97367view18:19, 11 May 2018AlexanderPicoupdating text color to make it visible
96978view18:20, 24 April 2018AlexanderPicoReverted to version '01:53, 8 March 2018' by AlexanderPico
96976view15:55, 24 April 2018WpblockedModified title
96310view08:53, 8 March 2018Mkutmonfix character encoding in references
96277view07:40, 5 March 2018EgonwConverted interactions to regular arrows, which were not mim:conversions.
96248view13:51, 2 March 2018Fehrhartconnected unconnected connections
96192view17:58, 23 February 2018Asios OliaModified description
96191view17:57, 23 February 2018Asios OliaModified description
96190view17:42, 23 February 2018Asios OliaModified description
96189view17:33, 23 February 2018Asios OliaModified description
95970view09:12, 11 February 2018EgonwIt had the PubChem CID from the start, but that entry is not the protein fibrin, but a small compound. I now took the Wikidata entry matching the proper Wikipedia page.
85340view11:14, 8 May 2016EgonwReplaced a mim-conversion with Arrow.
82707view08:59, 23 October 2015EgonwoxLDL has a separate identifier.
80971view13:17, 6 July 2015Mkutmonremove spaces in identifiers
79884view12:38, 23 April 2015Mkutmonremoved redundant publication xrefs
79878view11:43, 23 April 2015Mkutmonuse labels and graphical lines in legend
79872view14:53, 21 April 2015Mkutmonremoved invalid annotation for "Fibrinogen" (Database: Other)
70117view19:15, 12 July 2013MaintBotupdated to 2013 schema
69054view18:01, 8 July 2013EgonwReplaced an outdated HMDB identifier with the 3.5 one.
68769view16:12, 7 July 2013EgonwFixed the fibrin PubChem-compound data source name, Wikipedia identifier, and Enzyme Nomenclature data source names.
49537view09:35, 20 July 2012AndraCorrected Identifier error found in Rdf export
48238view06:00, 17 May 2012MaintBotUpdating PubChem xrefs
45013view18:13, 6 October 2011KhanspersOntology Term : 'pernicious anemia' added !
45012view18:07, 6 October 2011KhanspersOntology Term : 'Vitamin B12 (cobalamin) metabolic pathway' added !
41028view23:13, 1 March 2011MaintBotRemoved redundant pathway information and comments
39775view21:34, 17 January 2011AlexanderPicomore complete title
38840view17:36, 24 September 2010KhanspersAdded pathway links, changed line types
38839view17:34, 24 September 2010KhanspersPeriodical save, work in progress
37210view20:44, 21 May 2010KhanspersModified categories
37066view15:02, 15 May 2010DamarizEnd
37065view15:00, 15 May 2010DamarizFructosamine
37064view14:58, 15 May 2010DamarizHBA1
37063view14:54, 15 May 2010DamarizPAI-1
37062view14:52, 15 May 2010DamarizPeriodical save, work in progress

External references

DataNodes

View all...
NameTypeDatabase referenceComment
Methylmalonic acidMetaboliteHMDB0000202 (HMDB) Methylmalonate
S-AdenosylhomocysteineMetaboliteHMDB0000939 (HMDB)
S-AdenosylmethionineMetaboliteHMDB0001185 (HMDB)
Succinyl-CoAMetaboliteHMDB0001022 (HMDB)
5,10-Methylene-THFMetaboliteHMDB0001533 (HMDB) 5,10-Methylenetetrahydrofolate
5-methyl-THFMetaboliteHMDB0001396 (HMDB)
  • 5-methyltetrahydrofolate
  • Predominant food folate
8-Isoprostaglandin F2aMetaboliteHMDB0005083 (HMDB)
8-OHdGMetaboliteHMDB0003333 (HMDB) 8-Hydroxy-deoxyguanosine
ABCA1Protein19 (Entrez Gene) ATP-binding cassette, sub-family A (ABC1), member 1
ACTProtein12 (Entrez Gene)
  • alpha-1-antichymotrypsin
  • serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3
ALBProtein213 (Entrez Gene) albumin
APOA1-NO2TyrProtein335 (Entrez Gene) Nitrotyrosinated apolipoprotein A-I
APOA1Protein335 (Entrez Gene) apolipoprotein A-I
APOBProtein338 (Entrez Gene) apolipoprotein B
APOEProtein348 (Entrez Gene) apolipoprotein A-I
AdenosylcobalaminMetaboliteHMDB0002086 (HMDB)
Ascorbic acidMetaboliteCHEBI:29073 (ChEBI) Vitamin C
CBRProtein1.16.1.4 (Enzyme Nomenclature)
  • EC 1.16.1.4
  • cob(II)alamin reductase
CBSProtein875 (Entrez Gene)
  • EC 4.2.1.22
  • cystathionine-beta-synthase
CRPProtein1401 (Entrez Gene) C-reactive protein, pentraxin-related
CTHProtein1491 (Entrez Gene)
  • EC 4.4.1.1
  • cystathionase
CUBNGeneProduct8029 (Entrez Gene) cubilin (intrinsic factor-cobalamin receptor)
Cbl/HCMetaboliteHMDB0002174 (HMDB) Cobalamin haptocorrin complex
Cbl/IFMetaboliteHMDB0002174 (HMDB) Cobalamin Intrinsic factor complex
Cbl/TCMetaboliteHMDB0002174 (HMDB)
  • Cobalamin Transcobalamin complex
  • Holotranscobalamin
ChlorineMetaboliteHMDB0000492 (HMDB)
CholesterolMetaboliteHMDB0000067 (HMDB)
Cob(I)alaminMetaboliteHMDB0003429 (HMDB) Reduced cobalamin
Cob(II)alaminMetaboliteHMDB0006316 (HMDB) oxidized cobalamin
CreatinineMetaboliteHMDB0000562 (HMDB)
  • Creatine anhydride
  • A breakdown product of creatine phosphate in muscle
CystathionineMetaboliteHMDB0000099 (HMDB)
CysteineMetaboliteHMDB0000574 (HMDB)
D-Methylmalonyl-CoAMetaboliteHMDB0001269 (HMDB)
D-dimerProteinQ2162109 (Wikidata) http://en.wikipedia.org/wiki/Fibrin_degradation_product
DNA OxidationPathway
F2-IsoprostaneMetaboliteQ33659470 (Wikidata)
FADMetaboliteHMDB0001248 (HMDB) Flavin adenine dinucleotide
FGAProtein
FGBProtein
FGGProtein
Factor VIIProtein2155 (Entrez Gene)
  • EC 3.4.21.21
  • coagulation factor VII (serum prothrombin conversion accelerator)
FibrinProteinQ27205 (Wikidata)
FibrinogenProteinQ381899 (Wikidata)
FructosamineMetaboliteHMDB0002030 (HMDB)
GlucoseMetaboliteHMDB0000122 (HMDB)
H2O2MetaboliteHMDB0003125 (HMDB) Hydrogen peroxide
HBA1Protein3039 (Entrez Gene) hemoglobin, alpha 1
HBBProtein3043 (Entrez Gene) hemoglobin, beta
HCGeneProduct6947 (Entrez Gene)
  • Haptocorrin
  • transcobalamin I (vitamin B12 binding protein, R binder family)
HDL-CMetaboliteCHEBI:47775 (ChEBI)
  • high-density lipoprotein cholesterol
  • Cholesterol transport
HDL/APOA1MetaboliteCHEBI:39025 (ChEBI)
  • high-density lipoprotein
  • ApoA-I is present on the majority of HDL particles and constitutes aprox 70% of the apolipoprotein content of HDL particles
HDL/SAAMetaboliteCHEBI:39025 (ChEBI)
  • high-density lipoprotein
  • SAA circulates in plasma as a constituent of high density lipoproteins (HDL).
HDLMetaboliteCHEBI:39025 (ChEBI) high-density lipoprotein
HNO2MetaboliteCHEBI:25567 (ChEBI) Nitrous acid
HOClMetaboliteHMDB0001050 (HMDB) Hypochlorite
HbA1cProteinQ311213 (Wikidata)
  • Glycated hemoglobin
  • http://en.wikipedia.org/wiki/Glycated_hemoglobin
HomocysteineMetaboliteHMDB0000742 (HMDB)
IF*GeneProduct2694 (Entrez Gene)
  • gastric intrinsic factor (vitamin B synthesis)
  • Also known as GIF
IL10Protein3458 (Entrez Gene) interferon, gamma
IL1BProtein3553 (Entrez Gene) interleukin 1, beta
IL6Protein3569 (Entrez Gene) interleukin 6 (interferon, beta 2)
INSProtein3630 (Entrez Gene) Insulin
INSRProtein3643 (Entrez Gene) Insulin receptor
L-Methylmalonyl-CoAMetaboliteHMDB0001269 (HMDB)
LDL-CMetaboliteCHEBI:47774 (ChEBI)
  • low-density lipoprotein cholesterol
LDL/APOBMetaboliteCHEBI:39026 (ChEBI)
  • low-density lipoprotein
  • LDL particle contains 1 molecule of apo B
LDLMetaboliteCHEBI:39026 (ChEBI) low-density lipoprotein
LDLRProtein3949 (Entrez Gene) low density lipoprotein receptor
Lipid peroxidationPathwayWP1878 (WikiPathways)
Lipoprotein metabolismPathway
MATProtein4143 (Entrez Gene)
  • EC 2.5.1.6
  • Methionine adenosyltransferase
MCEEProtein84693 (Entrez Gene)
  • EC 5.1.99.1
  • methylmalonyl CoA epimerase
MCP1GeneProduct6347 (Entrez Gene)
  • Monocyte Chemotactic Protein 1
  • CCL2
MM-CoA-HProtein3.1.2.17 (Enzyme Nomenclature)
  • EC 3.1.2.17
  • (S)-methylmalonyl-CoA hydrolase
MMABProtein326625 (Entrez Gene)
  • EC 2.5.1.17
  • methylmalonic aciduria (cobalamin deficiency) cblB type
  • Also known as ATR
MPOProtein4353 (Entrez Gene)
  • EC 1.11.1.7
  • Myeloperoxidase
MSR*Protein4552 (Entrez Gene)
  • EC 1.16.1.8
  • 5-methyltetrahydrofolate-homocysteine methyltransferase reductase
MTHFR*Protein4524 (Entrez Gene)
  • 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
MTR*Protein4548 (Entrez Gene)
  • EC 2.1.1.13
  • 5-methyltetrahydrofolate-homocysteine methyltransferase
  • Also known as MS
MUTProtein4594 (Entrez Gene)
  • EC 5.4.99.2
  • methylmalonyl Coenzyme A mutase
  • Also known as MCM
MegalinGeneProduct4036 (Entrez Gene) Low density lipoprotein receptor-related protein 2
MethionineMetaboliteHMDB0000696 (HMDB)
Methylcob(III)alaminMetaboliteHMDB0002274 (HMDB)
N2OMetaboliteCHEBI:17045 (ChEBI)
  • Dinitrogen oxide
  • Nitrous oxide
NADHMetaboliteHMDB0001487 (HMDB) Reduced nicotinamide adenine diphosphate
NADMetaboliteHMDB0000902 (HMDB) Nicotinamide adenine dinucleotide
NADP+MetaboliteHMDB0000217 (HMDB) Nicotinamide adenine dinucleotide phosphate-Oxidized
NADPHMetaboliteHMDB0000221 (HMDB) Nicotinamide adenine dinucleotide phosphate-Reduced
NFKB1GeneProduct4790 (Entrez Gene) nuclear factor NF-kappa-B p50 subunit
NFKB2GeneProduct4791 (Entrez Gene) nuclear factor of kappa light polypeptide gene enhancer in B-cells 2
NO2MetaboliteCHEBI:33101 (ChEBI) Nitrogen dioxide
NO3-MetaboliteHMDB0002878 (HMDB) Nitrate
NOMetaboliteHMDB0003378 (HMDB) Nitric oxide
NitrotyrosineMetaboliteHMDB0001904 (HMDB)
O2MetaboliteHMDB0002168 (HMDB) Superoxide
O3MetaboliteCHEBI:25812 (ChEBI) ozone
ONOO-ONOOHMetaboliteHMDB0002179 (HMDB) Peroxynitrite
PAI-1Protein5054 (Entrez Gene) Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
PGE1MetaboliteHMDB0001442 (HMDB) Prostaglandin E1
PGE2MetaboliteHMDB0001220 (HMDB) Prostaglandin E2
PGF2aMetaboliteHMDB0001139 (HMDB) Prostaglandin F2a
PLGProtein5340 (Entrez Gene)
  • EC 3.4.21.7
  • Plasminogen
Prostaglandin metabolismPathwayWP98 (WikiPathways)
Protein tyrosine nitrationPathway
Pyridoxal 5'-phosphateMetaboliteHMDB0001491 (HMDB) Vitamin B6
RANTESProtein6352 (Entrez Gene)
  • CCL5
  • chemokine (C-C motif) ligand 5
RELAGeneProduct5970 (Entrez Gene) nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, p65
RiboflavinMetaboliteHMDB0000244 (HMDB)
SAA1Protein6288 (Entrez Gene) serum amyloid A1
SAA2Protein6289 (Entrez Gene) serum amyloid A2
SAA3Protein6290 (Entrez Gene) serum amyloid A3 pseudogene
SAA4Protein6291 (Entrez Gene) serum amyloid A4, constitutive
SHMTProtein6472 (Entrez Gene)
  • EC 2.1.2.1
  • Serine hydroxymethyltransferase
SOD1Protein6647 (Entrez Gene)
  • EC 1.15.1.1
  • superoxide dismutase 1, soluble
SOD2Protein6648 (Entrez Gene)
  • EC 1.15.1.1
  • superoxide dismutase 2, mitochondrial
SOD3Protein6649 (Entrez Gene)
  • EC 1.15.1.1
  • superoxide dismutase 3, extracellular
SRB1Protein949 (Entrez Gene) scavenger receptor class B, member 1
SerineMetaboliteHMDB0000187 (HMDB)
TAGMetaboliteCHEBI:17855 (ChEBI)
  • Triglyceride
  • Triacylglycerol
TCN2*GeneProduct6948 (Entrez Gene) transcobalamin II; macrocytic anemia
THFMetaboliteHMDB0001846 (HMDB) Tetrahydrofolic acid
TNFaProtein7124 (Entrez Gene) tumor necrosis factor (TNF superfamily, member 2)
ThrombinProtein2147 (Entrez Gene)
  • EC 3.4.21.5
  • coagulation factor II (thrombin)
Thromboxane A2MetaboliteHMDB0001452 (HMDB)
Thromboxane B2MetaboliteHMDB0003252 (HMDB)
VLDL-TAGMetaboliteCHEBI:47776 (ChEBI)
  • very-low-density lipoprotein-triglyceride
  • Triglyceride transport
VLDL/APOBMetaboliteCHEBI:39027 (ChEBI)
  • very-low-density lipoprotein
  • The VLDL is produced in the liver, contains one molecule of apoB100
VLDLMetaboliteCHEBI:39027 (ChEBI) very-low-density lipoprotein
Vitamin B12/CobalaminMetaboliteHMDB0002174 (HMDB)
ZincMetaboliteHMDB0015532 (HMDB)
a-TocopherolMetaboliteHMDB0001893 (HMDB) Vitamin E
oxLDLMetaboliteCHEBI:60151 (ChEBI) oxidized low-density lipoprotein
sICAM-1Protein3383 (Entrez Gene) soluble intercellular adhesion molecule 1
tPAProtein5327 (Entrez Gene)
  • EC 3.4.21.68
  • plasminogen activator, tissue
vitamin DMetaboliteCHEBI:27300 (ChEBI)

Annotated Interactions

No annotated interactions

Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP1533"
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