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somatic hypermutation of immunoglobulin genes
Definition
Target type: biologicalprocess
Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins. [GOC:add, ISBN:0781735149, PMID:11205330, PMID:11205333, PMID:14975236, PMID:7813007]
Somatic hypermutation (SHM) is a key process in the adaptive immune system, responsible for generating antibody diversity and enhancing the affinity of antibodies to their target antigens. This process occurs primarily in germinal centers (GCs) of secondary lymphoid organs, specifically within B cells that have been activated by antigen encounter.
SHM involves targeted mutations in the variable regions of immunoglobulin (Ig) genes, specifically the complementarity-determining regions (CDRs) which directly interact with antigens. These mutations are introduced by an enzyme called activation-induced cytidine deaminase (AID). AID deaminates cytosine bases in DNA to uracil, which is recognized and processed by cellular repair mechanisms.
The mechanism of SHM is highly targeted, relying on specific DNA sequences and the presence of transcription factors that mark the variable regions of Ig genes for AID-mediated deamination. AID activity is also regulated by various signaling pathways, ensuring that mutations occur in the appropriate context.
The mutations introduced by SHM can be either beneficial or detrimental. Beneficial mutations enhance the affinity of antibodies for their target antigens, leading to more effective immune responses. Detrimental mutations can disrupt the antibody's function, leading to its removal from the repertoire.
SHM is a highly error-prone process, resulting in a wide range of mutations with varying effects. This randomness is essential for generating the diversity of antibodies necessary to combat a wide range of pathogens. However, the process is also tightly controlled, ensuring that only a limited number of mutations are introduced, preventing the accumulation of deleterious mutations.
The selection process in GCs further refines the antibody repertoire. B cells with improved affinity for antigen are preferentially selected to proliferate and differentiate into memory B cells and plasma cells. This selection pressure drives the evolution of antibodies with increased affinity and specificity, shaping the immune response to specific pathogens.
In summary, SHM is a complex and critical process that ensures the generation of diverse and high-affinity antibodies, contributing significantly to the adaptive immune system's ability to recognize and neutralize a vast range of pathogens.'
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Proteins (3)
| Protein | Definition | Taxonomy |
|---|---|---|
| DNA polymerase lambda | A DNA polymerase lambda that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGP5] | Homo sapiens (human) |
| Single-stranded DNA cytosine deaminase | A single-stranded DNA cytosine deaminase that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9GZX7] | Homo sapiens (human) |
| DNA polymerase beta | A DNA polymerase beta that is encoded in the genome of human. [PRO:CNA] | Homo sapiens (human) |
Compounds (61)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| digallic acid | digallic acid: structure given in first source | benzoate ester; gallate ester | |
| hydroxylamine | amino alcohol : An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group. | hydroxylamines | algal metabolite; bacterial xenobiotic metabolite; EC 1.1.3.13 (alcohol oxidase) inhibitor; EC 4.2.1.22 (cystathionine beta-synthase) inhibitor; EC 4.3.1.10 (serine-sulfate ammonia-lyase) inhibitor; nitric oxide donor; nucleophilic reagent |
| aurintricarboxylic acid | aurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'. Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues. | monohydroxybenzoic acid; quinomethanes; tricarboxylic acid | fluorochrome; histological dye; insulin-like growth factor receptor 1 antagonist |
| chelerythrine | chelerythrine : A benzophenanthridine alkaloid isolated from the root of Zanthoxylum simulans, Chelidonium majus L., and other Papaveraceae. | benzophenanthridine alkaloid; organic cation | antibacterial agent; antineoplastic agent; EC 2.7.11.13 (protein kinase C) inhibitor |
| dequalinium | dequalinium : A quinolinium ion comprising decane in which one methyl hydrogen at each end of the molecule has been replaced by a 4-amino-2-methylquinolin-1-yl group. Dequalinium: A topical bacteriostat that is available as various salts. It is used in wound dressings and mouth infections and may also have antifungal action, but may cause skin ulceration. | quinolinium ion | antifungal agent; antineoplastic agent; antiseptic drug; mitochondrial NADH:ubiquinone reductase inhibitor |
| diphenyleneiodonium | dibenziodolium : An organic cation that is fluorene in which the methylene group is replaced by a positively charged iodine. diphenyleneiodonium: structure in first source; NADPH oxidase inhibitor | organic cation | |
| dipyridamole | dipyridamole : A pyrimidopyrimidine that is 2,2',2'',2'''-(pyrimido[5,4-d]pyrimidine-2,6-diyldinitrilo)tetraethanol substituted by piperidin-1-yl groups at positions 4 and 8 respectively. A vasodilator agent, it inhibits the formation of blood clots. Dipyridamole: A phosphodiesterase inhibitor that blocks uptake and metabolism of adenosine by erythrocytes and vascular endothelial cells. Dipyridamole also potentiates the antiaggregating action of prostacyclin. (From AMA Drug Evaluations Annual, 1994, p752) | piperidines; pyrimidopyrimidine; tertiary amino compound; tetrol | adenosine phosphodiesterase inhibitor; EC 3.5.4.4 (adenosine deaminase) inhibitor; platelet aggregation inhibitor; vasodilator agent |
| 2,3-dimethoxy-1,4-naphthoquinone | 2,3-dimethoxynaphthalene-1,4-dione : A naphthoquinone that is 1,4-naphthoquinone bearing two methoxy substituents at positions 2 and 3. Redox-cycling agent that induces intracellular superoxide anion formation and, depending on the concentration, induces cell proliferation, apoptosis or necrosis. Used to study the role of ROS in cell toxicity, apoptosis, and necrosis. | 1,4-naphthoquinones | |
| hydralazine | hydralazine : The 1-hydrazino derivative of phthalazine; a direct-acting vasodilator that is used as an antihypertensive agent. Hydralazine: A direct-acting vasodilator that is used as an antihypertensive agent. | azaarene; hydrazines; ortho-fused heteroarene; phthalazines | antihypertensive agent; vasodilator agent |
| phenelzine | Phenelzine: One of the MONOAMINE OXIDASE INHIBITORS used to treat DEPRESSION; PHOBIC DISORDERS; and PANIC. | primary amine | |
| beta-lapachone | beta-lapachone : A benzochromenone that is 3,4-dihydro-2H-benzo[h]chromene-5,6-dione substituted by geminal methyl groups at position 2. Isolated from Tabebuia avellanedae, it exhibits antineoplastic and anti-inflammatory activities. beta-lapachone: antineoplastic inhibitor of reverse transcriptase, DNA topoisomerase, and DNA polymerase | benzochromenone; orthoquinones | anti-inflammatory agent; antineoplastic agent; plant metabolite |
| mitoxantrone | mitoxantrone : A dihydroxyanthraquinone that is 1,4-dihydroxy-9,10-anthraquinone which is substituted by 6-hydroxy-1,4-diazahexyl groups at positions 5 and 8. Mitoxantrone: An anthracenedione-derived antineoplastic agent. | dihydroxyanthraquinone | analgesic; antineoplastic agent |
| protoporphyrin ix | protoporphyrin : A cyclic tetrapyrrole that consists of porphyrin bearing four methyl substituents at positions 3, 8, 13 and 17, two vinyl substituents at positions 7 and 12 and two 2-carboxyethyl substituents at positions 2 and 18. The parent of the class of protoporphyrins. protoporphyrin IX: RN given refers to parent cpd; structure in Merck Index, 9th ed, #7685 | ||
| sanguinarine | benzophenanthridine alkaloid : A specific group of isoquinoline alkaloids that occur only in higher plants and are constituents mainly of the Papaveraceae family. | alkaloid antibiotic; benzophenanthridine alkaloid; botanical anti-fungal agent | |
| tyrphostin a9 | alkylbenzene | geroprotector | |
| 1-naphthaldehyde | 1-naphthaldehyde : A naphthaldehyde with a formyl group at position 1. 1-naphthaldehyde: structure naphthaldehyde : An aldehyde in which the organyl group is a naphthyl group. | naphthaldehyde | mouse metabolite |
| pyrazolanthrone | anthra[1,9-cd]pyrazol-6(2H)-one : A member of the class of anthrapyrazoles that is anthra[1,9-cd]pyrazole substituted at position 6 by an oxo group. An inhibitor of c-Jun N-terminal kinase. pyrazolanthrone: JNK (c-Jun N-terminal kinase) inhibitor; structure in first source | anthrapyrazole; aromatic ketone; cyclic ketone | antineoplastic agent; c-Jun N-terminal kinase inhibitor; geroprotector |
| pamoic acid | pamoic acid: RN given refers to parent cpd; structure | dicarboxylic acid | |
| Dillapiole | 5-allyl 6,7-dimethoxy 1,3-benzodioxole: a plant based insecticide; structure in first source | benzodioxoles | metabolite |
| oleanolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | plant metabolite | |
| 2,3,5-trimethylquinol | 2,3,5-trimethylhydroquinone : A member of the class of hydroquinones that is hydroquinone substituted by methyl groups at positions 2, 3 and 5. 2,3,5-trimethylquinol: reducing agent | hydroquinones; methylbenzene | |
| ochracin | ochracin: produced by Aspergillus alutaceus; structure in first source | isochromanes | |
| zidovudine | zidovudine : A pyrimidine 2',3'-dideoxyribonucleoside compound having a 3'-azido substituent and thymine as the nucleobase. Zidovudine: A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia. | azide; pyrimidine 2',3'-dideoxyribonucleoside | antimetabolite; antiviral drug; HIV-1 reverse transcriptase inhibitor |
| idarubicin | Idarubicin: An orally administered anthracycline antineoplastic. The compound has shown activity against BREAST NEOPLASMS; LYMPHOMA; and LEUKEMIA. | anthracycline antibiotic; deoxy hexoside; monosaccharide derivative | |
| flupirtine | flupirtine: RN given refers to parent cpd without isomeric designation | aminopyridine | |
| ursolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | geroprotector; plant metabolite | |
| thymidine 5'-triphosphate | dTTP : A thymidine phosphate having a triphosphate group at the 5'-position. thymidine 5'-triphosphate: RN given refers to parent cpd | pyrimidine 2'-deoxyribonucleoside 5'-triphosphate; thymidine phosphate | Escherichia coli metabolite; mouse metabolite |
| betulinic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | anti-HIV agent; anti-inflammatory agent; antimalarial; antineoplastic agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; plant metabolite | |
| calanolide a | (+)-calanolide A : An organic heterotetracyclic compound that is 11,12-dihydro-2H,6H,10H-dipyrano[2,3-f:2',3'-h]chromen-2-one substituted by a hydroxy group at position 12, methyl groups at positions 6, 6, 10 and 11 and a propyl group at position 4 (the 10R,11S,12S stereoisomer). Isolated from Calophyllum lanigerum var austrocoriaceum and Calophyllum brasiliense, it exhibits potent activity against HIV-1 reverse transcriptase. calanolide A: NSC 661122 and costatolide are isomers; a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum (Clusiaceae); structure in first source | cyclic ether; delta-lactone; organic heterotetracyclic compound; secondary alcohol | HIV-1 reverse transcriptase inhibitor; plant metabolite |
| 2',3'-dideoxythymidine triphosphate | ddTTP : A pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate having thymine as the nucleobase. | pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate; thymidine phosphate | |
| 2',3'-dideoxyadenosine triphosphate | purine deoxyribonucleoside triphosphate | ||
| masoprocol | masoprocol : The meso-form of nordihydroguaiaretic acid. An antioxidant found in the creosote bush, Larrea divaricata, it is a potent lipoxygenase inhibitor that interferes with arachidonic acid metabolism. It also inhibits (though to a lesser extent) formyltetrahydrofolate synthetase, carboxylesterase, and cyclooxygenase. Masoprocol: A potent lipoxygenase inhibitor that interferes with arachidonic acid metabolism. The compound also inhibits formyltetrahydrofolate synthetase, carboxylesterase, and cyclooxygenase to a lesser extent. It also serves as an antioxidant in fats and oils. | nordihydroguaiaretic acid | antineoplastic agent; hypoglycemic agent; lipoxygenase inhibitor; metabolite |
| zidovudine triphosphate | |||
| illimaquinone | illimaquinone: structure given in first source; isolated from the Red Sea sponge Smenospongia; inhibits the RNase H. activity of HIV-1 reverse transcriptase | monohydroxy-1,4-benzoquinones; prenylquinone | metabolite |
| sitosterol, (3beta)-isomer | sitosterol : A member of the class of phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3. Sobatum: tradename; active fraction of Solanum trilobatum; reduces side-effects of radiation-induced toxicity | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; C29-steroid; phytosterols; stigmastane sterol | anticholesteremic drug; antioxidant; mouse metabolite; plant metabolite; sterol methyltransferase inhibitor |
| 2-(4-aminophenyl)quinoline | 2-(4-aminophenyl)quinoline: used for imaging tau protein; structure in first source | ||
| TTP | pyrimidine ribonucleoside 5'-triphosphate | ||
| aphidicolin | aphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication. Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells. | tetracyclic diterpenoid | antimicrobial agent; antimitotic; antineoplastic agent; antiviral drug; apoptosis inducer; Aspergillus metabolite; DNA synthesis inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; fungal metabolite |
| IPA-3 | IPA-3 : An organic disulfide obtained by oxidative dimerisation of 1-sulfanylnaphthalen-2-ol. | naphthols; organic disulfide | EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor |
| 2-[[2-methyl-5-(3-methyl-4-oxo-1-phthalazinyl)phenyl]sulfonylamino]acetic acid ethyl ester | alpha-amino acid ester | ||
| (2'-(4-aminophenyl)-(2,5'-bi-1h-benzimidazol)-5-amine) | benzimidazoles | ||
| nemadipine-a | nemadipine-A : A dihydropyridine that is that is 1,4-dihydropyridine which is substituted at positions 2 and 6 by methyl groups, at positions 3 and 5 by ethoxycarbonyl groups, and at position 4 by a pentafluorophenyl group. An L-type calcium channel alpha1-subunit antagonist. When exposed to the microscopic soil nematode Caenorhabditis elegans, nemadipine-A induces a variety of defects including those affecting morphology and egg laying. nemadipine-A: structure in first source | dicarboxylic acids and O-substituted derivatives; diester; dihydropyridine; ethyl ester; pentafluorobenzenes | calcium channel blocker |
| 5-[[(1-cyclohexyl-5-tetrazolyl)thio]methyl]-3-phenyl-1,2,4-oxadiazole | oxadiazole; ring assembly | ||
| ro 41-0960 | |||
| stigmasterol | stigmasta-5,22-dien-3-ol: isolated from freeze-dried powder of Blackberries (Rubus ursinus L.) which showed an activity on inhibition of chemocarcinogen stigmasterol : A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions. | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; phytosterols; stigmastane sterol | plant metabolite |
| tectochrysin | tectochrysin : A monohydroxyflavone that is flavone substituted by a hydroxy group at position 4 and a methoxy group at position 7 respectively. tectochrysin: structure in first source | monohydroxyflavone; monomethoxyflavone | antidiarrhoeal drug; antineoplastic agent; plant metabolite |
| pecilocin | pecilocin: fungicidal antibiotic produced by Paecilomyces varioti Bainier var. antibioticus; structure | N-acylpyrrolidine | |
| casein kinase ii | Casein Kinase II: A ubiquitous casein kinase that is comprised of two distinct catalytic subunits and dimeric regulatory subunit. Casein kinase II has been shown to phosphorylate a large number of substrates, many of which are proteins involved in the regulation of gene expression. | ||
| lyoniside | daucosterol : A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa. | beta-D-glucoside; monosaccharide derivative; steroid saponin | plant metabolite |
| corosolic acid | triterpenoid | metabolite | |
| oblongifolin c | oblongifolin C: has antineoplastic activity; isolated from Garcinia yunnanensis; structure in first source | ||
| edgeworin | edgeworin: from Dirca occidentalis Gray; structure given in first source | ||
| 2-(2-methoxyanilino)-8-[(3-methyl-1-piperidinyl)-oxomethyl]-[1,3,4]thiadiazolo[2,3-b]quinazolin-5-one | N-acylpiperidine | ||
| CDN1163 | CDN1163 : A secondary carboxamide resulting from the formal condensation of the carboxy group of 4-isopropoxybenzoic acid with the primary amino group of 2-methylquinolin-8-amine. An allosteric activator of sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA). CDN1163: a SERCA2 activator with antidiabetic activity; structure in first source | aromatic ether; quinolines; secondary carboxamide | SERCA activator |
| sch 725680 | Sch 725680: an aazaphilone from Aspergillus sp.; structure in first source | ||
| guttiferone k | guttiferone K: antiproliferative compound of Rheedia calcicola from the Madagascar rain forest; structure in first source | ||
| raltegravir | 1,2,4-oxadiazole; dicarboxylic acid amide; hydroxypyrimidine; monofluorobenzenes; pyrimidone; secondary carboxamide | antiviral drug; HIV-1 integrase inhibitor | |
| hispidin | hispidin : Fungal metabolite first found in basidiomycete Inonotus hispidus (formerly Polyporus hispidus). hispidin: metabolite of Basidiomycete Polyporus hispidus | 2-pyranones; catechols | antioxidant; EC 2.7.11.13 (protein kinase C) inhibitor; fungal metabolite |
| GS-443902 | GS-441524 triphosphate: intracellular active metabolite of remdesivir GS-443902 : An organic triphosphate that is GS-441524 in which the 5'-hydroxy group has been replaced by a triphosphate group. It is the active metabolite of remdesivir. | aromatic amine; C-nucleoside; nitrile; organic triphosphate; pyrrolotriazine | anticoronaviral agent; antiviral drug; drug metabolite |
| pinophilin b | pinophilin B: from cultures of a fungus (Penicillium pinophilum Hedgcok) derived from a seaweed; structure in first source | ||
| 4-[[(4-oxo-1,5,6,7-tetrahydrocyclopenta[d]pyrimidin-2-yl)thio]methyl]benzoic acid methyl ester | benzoate ester |