Homogentisate 1,2-dioxygenase

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homogentisate 1,2-dioxygenase
Illustration of Homogentisate 1,2-dioxygenase.jpg
3D rendering of Homogentisate Dioxygenase with active site amino acid residues and Iron atom colored. Histidine is the tan color, Glutamate the red color, and Iron is the blue.
Identifiers
EC no. 1.13.11.5
CAS no. 9029-49-6
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MetaCyc metabolic pathway
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Gene Ontology AmiGO / QuickGO
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NCBI proteins
homogentisate 1,2-dioxygenase (homogentisate oxidase)
Identifiers
SymbolHGD
Alt. symbolsAKU
NCBI gene 3081
HGNC 4892
OMIM 607474
RefSeq XM_001125882
UniProt Q93099
Other data
EC number 1.13.11.5
Locus Chr. 3 q21-q23
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Structures Swiss-model
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Homogentisate 1,2-dioxygenase (homogentisic acid oxidase, homogentisate oxidase, homogentisicase) is an enzyme which catalyzes the conversion of homogentisate to 4-maleylacetoacetate. Homogentisate 1,2-dioxygenase or HGD is involved in the catabolism of aromatic rings, more specifically in the breakdown of the amino acids tyrosine and phenylalanine. [1] HGD appears in the metabolic pathway of tyrosine and phenylalanine degradation once the molecule homogentisate is produced. Homogentisate reacts with HGD to produce maleylacetoacetate, which then is further used in the metabolic pathway. HGD requires the use of Fe2+ and O2 in order to cleave the aromatic ring of homogentisate. [2]

Contents

Enzyme active site

The active site of Homogentisate 1,2-dioxygenase was determined through the crystal structure, which was captured through the work of Titus et al. [1] Through the crystal structure the active site was found to contain the following residues; His292, His335, His365, His371, and Glu341.

Active Site of HGD containing His335, His371, Glu341, and the Fe atom Active site2.png
Active Site of HGD containing His335, His371, Glu341, and the Fe atom

Homogentisate binds in the active site to Glu341, His335, and His371 via the Fe2+ atom. The His292 binds to the hydroxyl group of the aromatic ring. His365 binds to Glu341 via hydrogen bonding to stabilize the amino acid side chains.

Pathology

Homegentisate 1,2 dioxygenase is involved in a type of metabolic diseases, called alkaptonuria. This disorder is due to the inability of the body to deal with homogentisate, which when oxidized by the body will produce the compound known as the ochronotic pigment, which causes a black color, and has several negative effects.[ citation needed ] This first of these effects is that the patient’s earwax will begin to turn black or red, depends on the patient’s diet, since the blood becomes oxidized and thus turns black due to excess of the ochronotic pigment. The other effect of the ochronotic pigment is that it can accumulate in the body’s connective tissue leading to degenerative arthritis, as the person grows older. [2] Alkaptonuria has another effect in that it can cause the urine to turn black as well if let to sit for long enough to become oxidized, though is this often a method for testing for the genetic defect. The metabolic disease is autosomal recessive, such that both parents must pass the gene on to their children in order for child to have the defect.[ citation needed ]

Mechanism

Borowski et al. propose a mechanism for HGD in their article featured in the Journal of the American Chemical Society. They base their mechanism on results from hybrid DFT calculations with B3LYP functionals using the programs Gaussian03 and Jaguar. The opening of the aromatic ring in homogentisate is a multi-step process. In the first two steps Fe2+ coordinates to the carbonyl and ortho phenol oxygens. The iron atom is also coordinated to His335, His371, and Glu341. O2 then binds to the iron atom, [2] subsequently reacting with the aromatic ring to form a peroxo-bridged intermediate.

In the next step, O2 is cleaved with the formation of an epoxide. This epoxide intermediate allowing radical reactions to eventually open and oxidize the six-membered ring.

Related Research Articles

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L-Tyrosine or tyrosine or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the Greek tyrós, meaning cheese, as it was first discovered in 1846 by German chemist Justus von Liebig in the protein casein from cheese. It is called tyrosyl when referred to as a functional group or side chain. While tyrosine is generally classified as a hydrophobic amino acid, it is more hydrophilic than phenylalanine. It is encoded by the codons UAC and UAU in messenger RNA.

<span class="mw-page-title-main">Catecholamine</span> Class of chemical compounds

A catecholamine is a monoamine neurotransmitter, an organic compound that has a catechol and a side-chain amine.

<span class="mw-page-title-main">Alkaptonuria</span> Medical condition

Alkaptonuria is a rare inherited genetic disease which is caused by a mutation in the HGD gene for the enzyme homogentisate 1,2-dioxygenase ; if a person inherits an abnormal copy from both parents, the body accumulates an intermediate substance called homogentisic acid in the blood and tissues. Homogentisic acid and its oxidized form alkapton are excreted in the urine, giving it an unusually dark color. The accumulating homogentisic acid causes damage to cartilage and heart valves, as well as precipitating as kidney stones and stones in other organs. Symptoms usually develop in people over 30 years old, although the dark discoloration of the urine is present from birth.

<span class="mw-page-title-main">Phenylalanine hydroxylase</span> Mammalian protein found in Homo sapiens

Phenylalanine hydroxylase. (PAH) (EC 1.14.16.1) is an enzyme that catalyzes the hydroxylation of the aromatic side-chain of phenylalanine to generate tyrosine. PAH is one of three members of the biopterin-dependent aromatic amino acid hydroxylases, a class of monooxygenase that uses tetrahydrobiopterin (BH4, a pteridine cofactor) and a non-heme iron for catalysis. During the reaction, molecular oxygen is heterolytically cleaved with sequential incorporation of one oxygen atom into BH4 and phenylalanine substrate. In humans, mutations in its encoding gene, PAH, can lead to the metabolic disorder phenylketonuria.

In chemistry, hydroxylation can refer to:

<span class="mw-page-title-main">Cysteine dioxygenase</span> Enzyme

Cysteine dioxygenase (CDO) is a non-heme iron enzyme that catalyzes the conversion of L-cysteine to cysteine sulfinic acid. CDO plays an important role in cysteine catabolism, regulating intracellular levels of cysteine and responding changes in cysteine availability. As such, CDO is highly regulated and undergoes large changes in concentration and efficiency. It oxidizes cysteine to the corresponding sulfinic acid by activation of dioxygen, although the exact mechanism of the reaction is still unclear. In addition to being found in mammals, CDO also exists in some yeast and bacteria, although the exact function is still unknown. CDO has been implicated in various neurodegenerative diseases and cancers, which is likely related to cysteine toxicity.

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<span class="mw-page-title-main">Homogentisic acid</span> Chemical compound

Homogentisic acid is a phenolic acid usually found in Arbutus unedo (strawberry-tree) honey. It is also present in the bacterial plant pathogen Xanthomonas campestris pv. phaseoli as well as in the yeast Yarrowia lipolytica where it is associated with the production of brown pigments. It is oxidatively dimerised to form hipposudoric acid, one of the main constituents of the 'blood sweat' of hippopotamuses.

<span class="mw-page-title-main">4-Hydroxyphenylpyruvate dioxygenase</span> Fe(II)-containing non-heme oxygenase

4-Hydroxyphenylpyruvate dioxygenase (HPPD), also known as α-ketoisocaproate dioxygenase, is an Fe(II)-containing non-heme oxygenase that catalyzes the second reaction in the catabolism of tyrosine - the conversion of 4-hydroxyphenylpyruvate into homogentisate. HPPD also catalyzes the conversion of phenylpyruvate to 2-hydroxyphenylacetate and the conversion of α-ketoisocaproate to β-hydroxy β-methylbutyrate. HPPD is an enzyme that is found in nearly all aerobic forms of life.

<span class="mw-page-title-main">Catechol 1,2-dioxygenase</span>

Catechol 1,2- dioxygenase is an enzyme that catalyzes the oxidative ring cleavage of catechol to form cis,cis-muconic acid:

<span class="mw-page-title-main">Aromatic amino acid</span> Amino acid having an aromatic ring

An aromatic amino acid is an amino acid that includes an aromatic ring.

<span class="mw-page-title-main">Fumarylacetoacetate hydrolase</span>

Fumarylacetoacetase is an enzyme that in humans is encoded by the FAH gene located on chromosome 15. The FAH gene is thought to be involved in the catabolism of the amino acid phenylalanine in humans.

In enzymology, a 3-hydroxy-2-methylpyridinecarboxylate dioxygenase (EC 1.14.12.4) is an enzyme that catalyzes the chemical reaction

In enzymology, a gentisate 1,2-dioxygenase (EC 1.13.11.4) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">L-amino-acid oxidase</span>

In enzymology, an L-amino acid oxidase (LAAO) (EC 1.4.3.2) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Maleylacetoacetate isomerase</span> Class of enzymes

In enzymology, maleylacetoacetate isomerase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Dioxygenase</span> Class of enzymes

Dioxygenases are oxidoreductase enzymes. Aerobic life, from simple single-celled bacteria species to complex eukaryotic organisms, has evolved to depend on the oxidizing power of dioxygen in various metabolic pathways. From energetic adenosine triphosphate (ATP) generation to xenobiotic degradation, the use of dioxygen as a biological oxidant is widespread and varied in the exact mechanism of its use. Enzymes employ many different schemes to use dioxygen, and this largely depends on the substrate and reaction at hand.

<span class="mw-page-title-main">3-Maleylpyruvic acid</span> Chemical compound

3-Maleylpyruvic acid, or 3-maleylpyruvate, is a dicarboxylic acid formed by the oxidative ring opening of gentisic acid by gentisate 1,2-dioxygenase during the metabolism of tyrosine. It is converted into 3-fumarylpyruvate by maleylpyruvate isomerase.

<span class="mw-page-title-main">Galactose oxidase</span>

Galactose oxidase is an enzyme that catalyzes the oxidation of D-galactose in some species of fungi.

<span class="mw-page-title-main">4-Hydroxyphenylglycine</span> Chemical compound

4-Hydroxyphenylglycine (HPG) is a non-proteogenic amino acid found in vancomycin and related glycopeptides. HPG is synthesized from the shikimic acid pathway and requires four enzymes to synthesize: Both L- and D-HPG are used in the vancomycin class of antibiotics. Tyrosine, a similar amino acid, differs by a methylene group (CH2) between the aromatic ring and the alpha carbon.

References

  1. 1 2 Titus GP, Mueller HA, Burgner J, Rodríguez De Córdoba S, Peñalva MA, Timm DE (Jul 2000). "Crystal structure of human homogentisate dioxygenase". Nature Structural Biology. 7 (7): 542–6. doi:10.1038/76756. hdl: 10261/71724 . PMID   10876237. S2CID   6219553.
  2. 1 2 3 Borowski T, Georgiev V, Siegbahn PE (Dec 2005). "Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study". Journal of the American Chemical Society. 127 (49): 17303–14. doi:10.1021/ja054433j. PMID   16332080.