Summary: Histidine carboxylase PI chain
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Histidine decarboxylase Edit Wikipedia article
Cartoon depiction of C-truncated HDC dimer with PLP residing in active site.
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Histidine decarboxylase (HDC) is an enzyme responsible for catalyzing the decarboxylation of histidine to form histamine. In mammals, histamine is an important biogenic amine with regulatory roles in neurotransmission, gastric acid secretion and immune response. Histidine decarboxylase is the sole member of the histamine synthesis pathway, producing histamine in a one-step reaction. Histamine cannot be generated by any other known enzyme. HDC is therefore the primary source of histamine in most mammals and eukaryotes. The enzyme employs a pyridoxal 5'-phosphate cofactor, in similarity to many amino acid decarboxylases. Eukaryotes, as well as gram-negative bacteria share a common HDC, while gram-positive bacteria employ an evolutionarily unrelated pyruvoyl-dependent HDC. In humans, histidine decarboxylase is encoded by the HDC gene.
Histidine decarboxylase is a group II pyridoxal-dependent decarboxylase, along with aromatic-L-amino-acid decarboxylase, and tyrosine decarboxylase. HDC is expressed as a 74 kDa polypeptide which is not enzymatically functional. Only after post-translational processing does the enzyme become active. This processing consists of truncating much of the protein's C-terminal chain, reducing the peptide molecular weight to 54 kDa.
Histidine decarboxylase exists as a homodimer, with several amino acids from the respective opposing chain stabilizing the HDC active site. In HDC's resting state, PLP is covalently bound in a Schiff base to lysine 305, and stabilized by several hydrogen bonds to nearby amino acids aspartate 273, serine 151 and the opposing chain's serine 354. HDC contains several regions that are sequentially and structurally similar to those in a number of other pyridoxal-dependent decarboxylases. This is particularly evident in the vicinity of the active site lysine 305.
HDC decarboxylates histidine through the use of a PLP cofactor initially bound in a Schiff base to lysine 305. Histidine initiates the reaction by displacing lysine 305 and forming a aldimine with PLP. Histidine's carboxyl group then leaves, forming carbon dioxide. Finally, PLP re-forms its original Schiff base at lysine 305, and histamine is released. This mechanism is very similar to those employed by other pyridoxal-dependent decarboxylases. In particular, the aldimine intermediate is a common feature of all known PLP-dependent decarboxylases. HDC is highly specific for its histidine substrate.
Histidine decarboxylase is the primary biological source of histamine. Histamine is an important biogenic amine that moderates numerous physiologic processes. There are four different histamine receptors, H1, H2, H3, and H4, each of which carries a different biological significance. H1 modulates several functions of the central and peripheral nervous system, including circadian rhythm, body temperature and appetite. H2 activation results in gastric acid secretion and smooth muscle relaxation. H3 controls histamine turnover by feedback inhibition of histamine synthesis and release. Finally, H4 plays roles in mast cell chemotaxis and cytokine production.
In humans, HDC is primarily expressed in mast cells and basophil granulocytes. Accordingly, these cells contain the body's highest concentrations of histamine granules. No-mast cell histamine is also found in the brain, where it is used as a neurotransmitter.
Antihistamines are a class of medications designed to reduce unwanted effects of histamine in the body. Typical antihistamines block specific histamine receptors, depending on what physiological purpose they serve. For example, diphenhydramine (Benadryl™), targets and inhibits the H1 histamine receptor to relieve symptoms of allergic reactions. Inhibitors of histidine decarboxylase can conceivably be used as atypical antihistamines. Tritoqualine, as well as various catechins, such as epigallocatechin-3-gallate, a major component of green tea, have been shown to target HDC and histamine-producing cells, reducing histamine levels and providing anti-inflammatory, anti-tumoral, and anti-angiogenic effects.
- Aromatic L-amino acid decarboxylase
- Tyrosine decarboxylase
- Pyridoxal 5'-phosphate
- Mast cell
- Epps HM (1945). "Studies on bacterial amino-acid decarboxylases: 4. l(-)-histidine decarboxylase from Cl. welchii Type A". Biochem. J. 39 (1): 42–6. PMC . PMID 16747851.
- "Entrez Gene: histidine decarboxylase".
- Shahid, Mohammad (2009). "Histamine, Histamine Receptors, and their Role in Immunomodulation: An Updated Systematic Review" (PDF). The Open Immunology Journal. 2: 9–41.
- Riley WD, Snell EE (October 1968). "Histidine decarboxylase of Lactobacillus 30a. IV. The presence of covalently bound pyruvate as the prosthetic group". Biochemistry. 7 (10): 3520–8. doi:10.1021/bi00850a029. PMID 5681461.
- Rosenthaler J, Guirard BM, Chang GW, Snell EE (July 1965). "Purification and properties of histidine decarboxylase from Lactobacillus 30a". Proc. Natl. Acad. Sci. U.S.A. 54 (1): 152–8. doi:10.1073/pnas.54.1.152. PMC . PMID 5216347.
- Kimura, B.; Takahashi, H.; Hokimoto, S.; Tanaka, Y.; Fujii, T. (2009-08-01). "Induction of the histidine decarboxylase genes of Photobacterium damselae subsp. damselae (formally P. histaminum) at low pH". Journal of Applied Microbiology. 107 (2): 485–497. doi:10.1111/j.1365-2672.2009.04223.x. ISSN 1365-2672.
- Bruneau G, Nguyen VC, Gros F, Bernheim A, Thibault J (November 1992). "Preparation of a rat brain histidine decarboxylase (HDC) cDNA probe by PCR and assignment of the human HDC gene to chromosome 15". Hum. Genet. 90 (3): 235–8. doi:10.1007/bf00220068. PMID 1487235.
- Komori, Hirofumi; Nitta, Yoko; Ueno, Hiroshi; Higuchi, Yoshiki (2012-08-17). "Structural Study Reveals That Ser-354 Determines Substrate Specificity on Human Histidine Decarboxylase". Journal of Biological Chemistry. 287 (34): 29175–29183. doi:10.1074/jbc.M112.381897. ISSN 0021-9258. PMC . PMID 22767596.
- Nitta, Yoko (2010). "Expression of recombinant human histidine decarboxylase with full length and C-terminal truncated forms in yeast and bacterial cells" (PDF). J. Biol. Macromol. 10.
- Jackson, F. Rob (1990-10-01). "Prokaryotic and eukaryotic pyridoxal-dependent decarboxylases are homologous". Journal of Molecular Evolution. 31 (4): 325–329. doi:10.1007/BF02101126. ISSN 0022-2844.
- Sandmeier, Erika; Hale, Terence I.; Christen, Philipp (1994-05-01). "Multiple evolutionary origin of pyridoxal-5′-phosphate-dependent amino acid decarboxylases". European Journal of Biochemistry. 221 (3): 997–1002. doi:10.1111/j.1432-1033.1994.tb18816.x. ISSN 1432-1033.
- Wu, Fang; Yu, Jing; Gehring, Heinz (2008-03-01). "Inhibitory and structural studies of novel coenzyme-substrate analogs of human histidine decarboxylase". The FASEB Journal. 22 (3): 890–897. doi:10.1096/fj.07-9566com. ISSN 0892-6638. PMID 17965265.
- "Pyridoxal phosphate-dependent decarboxylase". InterPro.
- Toney, Michael D. (2005-01-01). "Reaction specificity in pyridoxal phosphate enzymes". Archives of Biochemistry and Biophysics. Highlight issue on Enzyme Mechanisms. 433 (1): 279–287. doi:10.1016/j.abb.2004.09.037.
- Panula, Pertti; Chazot, Paul L.; Cowart, Marlon; Gutzmer, Ralf; Leurs, Rob; Liu, Wai L. S.; Stark, Holger; Thurmond, Robin L.; Haas, Helmut L. (2015-07-01). "International Union of Basic and Clinical Pharmacology. XCVIII. Histamine Receptors". Pharmacological Reviews. 67 (3): 601–655. doi:10.1124/pr.114.010249. ISSN 1521-0081. PMC . PMID 26084539.
- Canonica, G. Walter; Blaiss, Michael (2011-02-23). "Antihistaminic, Anti-Inflammatory, and Antiallergic Properties of the Nonsedating Second-Generation Antihistamine Desloratadine: a Review of the Evidence". World Allergy Organization Journal. 4 (2): 47. doi:10.1097/WOX.0b013e3182093e19. ISSN 1939-4551. PMC . PMID 23268457.
- Hill, S.J. (1997). "Classification of Histamine Receptors". Pharmacological Reviews. 49: 253–278 – via ASPET.
- West, R. E.; Zweig, A.; Shih, N. Y.; Siegel, M. I.; Egan, R. W.; Clark, M. A. (1990-11-01). "Identification of two H3-histamine receptor subtypes". Molecular Pharmacology. 38 (5): 610–613. ISSN 0026-895X. PMID 2172771.
- Blandina, Patrizio; Provensi, Gustavo; Munari, Leonardo; Passani, Maria Beatrice (2012-01-01). "Histamine neurons in the tuberomamillary nucleus: a whole center or distinct subpopulations?". Frontiers in Systems Neuroscience. 6. doi:10.3389/fnsys.2012.00033. ISSN 1662-5137. PMC . PMID 22586376.
- "Diphenhydramine Hydrochloride". Drugs.com.
- Melgarejo, Esther; Medina, Miguel Ángel; Sánchez-Jiménez, Francisca; Urdiales, José Luis (2010-09-01). "Targeting of histamine producing cells by EGCG: a green dart against inflammation?". Journal of Physiology and Biochemistry. 66 (3): 265–270. doi:10.1007/s13105-010-0033-7. ISSN 1138-7548.
- "Online Mendelian Inheritance in Man: histidine decarboxylase".
- Need AC, Keefe RS, Ge D, et al. (2009). "Pharmacogenetics of antipsychotic response in the CATIE trial: a candidate gene analysis.". Eur. J. Hum. Genet. 17 (7): 946–57. doi:10.1038/ejhg.2008.264. PMC . PMID 19156168.
- Masini E, Fabbroni V, Giannini L, et al. (2005). "Histamine and histidine decarboxylase up-regulation in colorectal cancer: correlation with tumor stage.". Inflamm. Res. 54 Suppl 1: S80–1. doi:10.1007/s00011-004-0437-3. PMID 15928846.
- Li Z, Liu J, Tang F, et al. (2008). "Expression of non-mast cell histidine decarboxylase in tumor-associated microvessels in human esophageal squamous cell carcinomas.". APMIS. 116 (12): 1034–42. doi:10.1111/j.1600-0463.2008.01048.x. PMID 19133005.
- Szafranski K, Schindler S, Taudien S, et al. (2007). "Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns.". Genome Biol. 8 (8): R154. doi:10.1186/gb-2007-8-8-r154. PMC . PMID 17672918.
- Ai W, Liu Y, Langlois M, Wang TC (2004). "Kruppel-like factor 4 (KLF4) represses histidine decarboxylase gene expression through an upstream Sp1 site and downstream gastrin responsive elements.". J. Biol. Chem. 279 (10): 8684–93. doi:10.1074/jbc.M308278200. PMID 14670968.
- Raychowdhury R, Fleming JV, McLaughlin JT, et al. (2002). "Identification and characterization of a third gastrin response element (GAS-RE3) in the human histidine decarboxylase gene promoter.". Biochem. Biophys. Res. Commun. 297 (5): 1089–95. doi:10.1016/S0006-291X(02)02345-8. PMID 12372397.
- Kimura K, Wakamatsu A, Suzuki Y, et al. (2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.". Genome Res. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC . PMID 16344560.
- Sköldberg F, Portela-Gomes GM, Grimelius L, et al. (2003). "Histidine decarboxylase, a pyridoxal phosphate-dependent enzyme, is an autoantigen of gastric enterochromaffin-like cells.". J. Clin. Endocrinol. Metab. 88 (4): 1445–52. doi:10.1210/jc.2002-021761. PMID 12679420.
- Brew O, Lakasing L, Sullivan M (2007). "Differential activity of histidine decarboxylase in normal and pre-eclamptic placentae.". Placenta. 28 (5-6): 585–7. doi:10.1016/j.placenta.2006.05.003. PMID 16822545.
- Zhang F, Xiong DH, Wang W, et al. (2006). "HDC gene polymorphisms are associated with age at natural menopause in Caucasian women.". Biochem. Biophys. Res. Commun. 348 (4): 1378–82. doi:10.1016/j.bbrc.2006.08.008. PMC . PMID 16919600.
- Tippens AS, Gruetter CA (2004). "Detection of histidine decarboxylase mRNA in human vascular smooth muscle and endothelial cells.". Inflamm. Res. 53 (6): 215–6. doi:10.1007/s00011-004-1252-6. PMID 15167966.
- Siezen CL, Bont L, Hodemaekers HM, et al. (2009). "Genetic susceptibility to respiratory syncytial virus bronchiolitis in preterm children is associated with airway remodeling genes and innate immune genes.". Pediatr. Infect. Dis. J. 28 (4): 333–5. doi:10.1097/INF.0b013e31818e2aa9. PMID 19258923.
- Morgan TK, Montgomery K, Mason V, et al. (2006). "Upregulation of histidine decarboxylase expression in superficial cortical nephrons during pregnancy in mice and women.". Kidney Int. 70 (2): 306–14. doi:10.1038/sj.ki.5001553. PMID 16760908.
- Papadopoulou N, Kalogeromitros D, Staurianeas NG, et al. (2005). "Corticotropin-releasing hormone receptor-1 and histidine decarboxylase expression in chronic urticaria.". J. Invest. Dermatol. 125 (5): 952–5. doi:10.1111/j.0022-202X.2005.23913.x. PMID 16297195.
- Janssen R, Bont L, Siezen CL, et al. (2007). "Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes.". J. Infect. Dis. 196 (6): 826–34. doi:10.1086/520886. PMID 17703412.
- Strausberg RL, Feingold EA, Grouse LH, et al. (2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC . PMID 12477932.
- Aichberger KJ, Mayerhofer M, Vales A, et al. (2006). "The CML-related oncoprotein BCR/ABL induces expression of histidine decarboxylase (HDC) and the synthesis of histamine in leukemic cells.". Blood. 108 (10): 3538–47. doi:10.1182/blood-2005-12-028456. PMID 16849647.
- Lee JK, Kim HT, Cho SM, et al. (2003). "Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population.". J. Hum. Genet. 48 (5): 213–6. doi:10.1007/s10038-003-0011-9. PMID 12768436.
- Jeong HJ, Moon PD, Kim SJ, et al. (2009). "Activation of hypoxia-inducible factor-1 regulates human histidine decarboxylase expression.". Cell. Mol. Life Sci. 66 (7): 1309–19. doi:10.1007/s00018-009-9001-1. PMID 19266161.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Histidine carboxylase PI chain Provide feedback
Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6.
Coton E, Rollan GC, Lonvaud-Funel A; , J Appl Microbiol 1998;84:143-151.: Histidine carboxylase of Leuconostoc oenos 9204: purification, kinetic properties, cloning and nucleotide sequence of the hdc gene. PUBMED:9633629 EPMC:9633629
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003427
Histidine decarboxylase (EC) catalyses the formation of histamine from histidine [PUBMED:11243783]. It requires a pyruvoyl group for its activity. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta) 6 by nonhydrolytic self-catalysis.
In Lactobacillus cells, pyruvoyl-dependent histidine decarboxylase functions to counter the effects of acidic fermentation products, thus modifying extracellular pH. Cells take up histidine and decarboxylate it using histidine decarboxylase to consume a proton and produce histamine, which the cells excrete. These proteins are all dependent on the pyruvoyl cofactor, which is part of the active site and is located at the amino terminus of the alpha-chain (corresponding to residue 82 of the proenzyme in Lactobacillus sp. 30a), at the break between the beta and alpha chains. This pyruvoyl cofactor facilitates decarboxylation via a Schiff base mechanism resembling that of the more common PLP-dependent decarboxylases. This covalent intermediate allows for resonance stabilisation, facillitaing the decarboxylation step. The mechanism for this enzyme can be found in MACiE entry M0049 [PUBMED:2745463, PUBMED:8490030, PUBMED:2197977].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||histidine decarboxylase activity (GO:0004398)|
|Biological process||histidine metabolic process (GO:0006547)|
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_19599 (release 5.2)|
|Author:||Mian N, Bateman A|
|Number in seed:||5|
|Number in full:||33|
|Average length of the domain:||260.20 aa|
|Average identity of full alignment:||42 %|
|Average coverage of the sequence by the domain:||93.27 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HDC domain has been found. There are 34 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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