Serine dehydratase
| serine dehydratase | |||||||
|---|---|---|---|---|---|---|---|
| Identifiers | |||||||
| Symbol | SDS | ||||||
| NCBI gene | 10993 | ||||||
| HGNC | 10691 | ||||||
| OMIM | 182128 | ||||||
| RefSeq | NM_006843 | ||||||
| UniProt | P20132 | ||||||
| Other data | |||||||
| EC number | 4.3.1.17 | ||||||
| Locus | Chr. 12 q24.21 | ||||||
| |||||||
Serine Dehydratase or L-Serine Ammonia Lyase (SDH) is in the family of Pyridoxal Phosphate-dependent (PLP) enzymes. SDH is found widely in nature, but its structural and chemical properties are considerably different from species to species. SDH is found in yeast, bacteria, and the cytoplasm of mammalian hepatocytes. The mechanism it catalyzes is the deamination of L-serine and L-threonine to yield pyruvate and α-ketobutyrate respectively, with the release of ammonia in both cases. [1]
Conversion of L-serine and L-threonine to pyruvate and α-ketobutyrate, respectively.
This enzyme has 1 substrate, L-Serine, and two products, pyruvate and NH3, and uses 1 cofactor, pyridoxal phosphate (PLP).
Nomenclature
Serine Dehydratase is also known as[2]: L-serine ammonia-lyase; Serine deaminase; L-hydroxyaminoacid dehydratase; L-serine deaminase; L-serine dehydratase; L-serine hydro-lyase
Enzyme Structure
HoloEnzyme: The holoenzyme SDH contains 319 residues, 1 PLP cofactor molecule, and 131 water molecules1. The overall fold of the monomer is very similar to that of other PLP-dependent enzymes of the Beta-family . The enzyme contains a large domain (catalytic domain or PLP- binding domain) and a small domain. The domains are joined by two peptide linkers (residues 32-35 and 138-146), with the internal gap created being the space for the active site[1] (Figure 1).
Two Dimers: Two monomers of hSDS (human SDH) come together to make a dimer. The interface between the two monomers is formed through hydrogen bonds and hydrophobic interactions. The monomer–monomer contacts involve six pairs of hydrogen bonds formed between 10 residues (Arg98-Asn260, Leu310-Asn260, and Leu265-Lys263). Additional interactions include a number of hydrophobic contacts between the residues Met17, Lys21, Asn101, Glu102, Ser306, Ile308, Ser309, and Ile264 in each monomer.[1] (Figure 2)
Cofactor Binding Site: The PLP cofactor is positioned in between the Beta-strands 7 and 10 of the large domain and lies on the large internal gap made between small and large domain. The cofactor is covalently bonded through a Schiff base linkage to Lys41. The cofactor is sandwiched between the side chain of Phe40 and the main chain of Ala222. Each of the polar substituents of PLP is coordinated by functional groups: the pyridinium nitrogen of PLP is hydrogen-bonded to the side chain of Cys303, the C3-hydroxyl group of PLP is hydrogen-bonded to the side chain of Asn67, and the phosphate group of PLP is coordinated by main chain amides from the tetraglycine loop.[1] (Figure 3 and Figure 4)
Figure 3 shows the mechanism of converting L-Serine into Pyruvate, showing the SDH active site, PLP coenzyme and substrate.[1]
File:MechanismofSerineDehydratasebonds.pdf
Figure 4 shows the role of SDH in orienting the PLP molecule perpendicular to the substrate Serine.
Enzyme Mechanism
The degradation of serine to pyruvate is an example of a pyridoxal phosphate-dependent (PLP) catalyzed Beta-elimination reaction. Beta-eliminations mediated by PLP yields products that have undergone a two-electron oxidation at C-alpha. In general, beta-eliminations involve the halide leaving and a proton is removed from the adjacent beta-carbon to give a double bond; thus the origin of the pi electrons are from the C-H bond on the beta carbon. Beta eliminations occur with no net oxidation or reduction of PLP. In overall terms, the reaction catalyzed by serine dehydratase involves two steps: catalytic elimination and a nonenzymatic hydrolysis reaction. The main role of SDH is to lower the activation energy of this reaction by binding the coenzyme and substrate in a particular conformation geometry.
Steps[3] :
(In panel 1 of Figure 5) In the SDH enzyme’s active site, Lys41 is located above the PLP molecule with it’s R group NH2 connected to C4 of PLP by a Schiff base linkage. The phosphate group of PLP is located in a pocket of G residues. Serine enters the active site and is involved in an ionic interaction between its positively charged amino group and the negatively charged phosphate group of PLP. The intermediate PLP-Ser aldimine is created. SDH orients the serine molecule’s Calpha-H parallel to the overlapping 2p orbitals in the PLP pi system; in other words, SDH holds serine perpendicular to the plane of the PLP ring.[3] (Figure 6)
(In panel 2 of Figure 5) The amino group of serine protonates the PLP phosphate by forming a H-bond. The deprotonated amino group of Serine is now a good nucleophile that attacks the Lys-PLP Schiff base C4 carbon (shown in panel 1). The intermediate PLP-Ser aldimine is created and Lys41 is released from PLP. [3]
(In panel 3 of Figure 5) The COOH group of serine is positioned tightly in the SDH enzyme, so that the serine molecule is perpendicular to the PLP pi system. The R group OH group participates in two hydrogen bonds with SDH’s Ala222 and the protonated phosphate of PLP. The protonated phosphate of PLP acts as an acid and donates it’s protons to hydroxyl of serine. In a concerted fashion, the R hydrogen of serine is removed by Lys41 and water is released. The intermediate created is PLP-aminoacrylate.[3]
In the reaction as the water leaves from the Beta carbon, the SDH orients the bond perpendicular to the PLP plane (Figure 6). This allows the new pi bonds between Calpha and Cbeta to form resonance with the PLP pi system.[3] (Figure 6)
(In panel 4 of Figure 5) Lys41 from SDH attacks C4, forming a tetrahedral intermediate. A Schiff base linkage is then made. [3]
(In panel 5 of Figure 5) A Schiff base linkage is then made and the aminoacrylate group is released as pyruvate. [3]
(In panel 6 of Figure 5) The aminoacrylate released from PLP is unstable in aqueous solution and rapidly [[tautomerizes]] to the preferred imine form; this is spontaneously hydrolyzed to yield alpha-keto acid product of pyruvate. The aminoacrylate is nonezymatically [[deaminated]] to pyruvate by hydrolysis. The enzyme-PLP Schiff base linkage is reformed. [3]
Inhibitors
According to the series of assays by Cleland (1967), the linear rate of pyruvate formation at various concentrations of inhibitors demonstrates that L-cysteine and D-serine competitively inhibit the enzyme SDH[4] . Insulin is known to accelerate glycolysis and repress induction of liver serine dehydratase in adult diabetic rats.[5] Studies have been conducted to show insulin causes a 40-50% inhibition of the induction serine dehydratase by glucagon in hepatocytes of rats.[6]
Biological Function
In general, the SDH level decreases with increasing mammalian size[7].In fact, mammals catabolize serine into pyruvate with the enzymes serine hydroxymethyltransferase and glycine cleavage enzymes rather than SDH.
Studies show that SDH from rat hepatocytes plays an important role in gluconeogenesis; its activity is augmented by high-protein diets and starvation.During periods of low carbohydrates, serine is converted into pyruvate via SDH. This pyruvate enters the mitochondria where it can be converted into oxaloacetate, and, thus, glucose. [8]
However, interestingly, little is known about the properties and the function of human SDH because human liver has low SDH activity. In a study done by Yoshida and Kikuchi, routes of glycine breakdown were measured. Glycine can be comverted into serine and either become pyruvate via serine dehydratase or undergo oxidative cleavage into methylene-THF, ammonia, and carbon dioxide. Results showed the secondary importance of the SDH pathway. [8][9]
Disease Relevance
Although there is much controversy over the role of SDH in human hepatocytes, studies have shown that nonketotic hyperglycemia is due to the deficiency of threonine dehydratase, a close corollary to serine dehydratase. Serine dehydratase has also been found to be absent in human colon carcinoma and rat sarcoma. The observed enzyme imbalance in these tumors ensures that an increased capacity for the synthesis of serine is coupled to its utilization for nucleotide biosynthesis as a part of the biochemical commitment to cellular replication in cancer cells. This pattern is found in sarcomas and carcinomas, and in tumors of human and rodent origin Thus, SDH has significance in the development of hyperglycemia and tumors.[10]
In addition, homocystinuria is a hereditary disease caused by the deficiency of L-serine dehydratase. Its symptoms include mental retardation, death, atherosclerosis, and coronary thrombosis as well as dislocation of the eye lens. Homocystinuria is a disease characterized by high urine and plasma levels of homocysteine. L-Serine dehydratase condenses homocysteine with serine to form cystathionine. [11]
Evolution
Comparing human and rat serine dehydratase using a cDNA library was identical except for a 36 amino acid residue. The overall homology between rat SDH and human SDH is 81% in the nucleotide sequence and 84% in the amino acid sequence. Similarities have also been shown between yeast and E.Coli threonine dehydratase and human serine dehydratase. Human SDH shows sequence homology of 27% with the yeast enzyme and 27% with the E. Coli enzyme[12].
Additionally, the primary structures are shown to be similar between mammalian SDH and microbial threonine dehydratase, especially in the sequences surrounding the PLP cofactor and the G-residues surrounding the PLP’s phosphate group. Thus, in PLP enzymes, there is high conservation of the active site residues during evolution. With active site sequence conservation, it is suggested that hydroxyamino and dehydratase originated from a common ancestor. [12]
In an analysis done by Mehta and Christen from the Center for Bioinformatics and Biotechnology, the pyridoxal-5-phosphate (vitamin B6)-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. The overall B6 enzymes diverged into four independent evolutionary lines: α family (i.e. aspartate aminotransferase), β family (serine dehydratase),D-alanine aminotransferase family and the alanine racemase family. An example of the evolutionary similarity in the Beta family is seen in the mechanism. The β enzymes are all lyases and catalyze reactions where Cα and Cβ participate. Overall, in the PLP-dependent enzymes, the PLP in every case is covalently attached via an imine bond to the amino group in the active site. [13]
External links
- Serine+dehydratase at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
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References
- ^ a b c d e Lei, Sun (2005). "Crystal structure of the pyridoxal-5′-phosphate-dependent serine dehydratase from human liver" (PDF). Protein Science. 3. 14: 791–798. PMID PMC2279282. Retrieved 17 May 2011.
{{cite journal}}: Check|pmid=value (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ "KEGG ENZYME Database Entry". Kyoto Encyclopedia of Genes and Genomes. Kanehisa Laboratories. Retrieved 17 May 2011.
- ^ a b c d e f g h Yamada, Taro (11). "Crystal Structure of Serine Dehydratase from Rat Liver". Biochemistry. 44. 42: 12854–12865. PMID 14596599. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Text "Henry C. Pitot,⊥ and Fusao Takusagawa" ignored (help)CS1 maint: extra punctuation (link) - ^ Gannon, Frank (1). "L-Serine Dehydratase from Arthrobacter globiformis" (PDF). Biochemistry Journal. 2. 161: 345–355. PMID 322657. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Freedland, R.A. (23). "Studies on glucose-6-phosphatase and glutaminase in rat liver and kidney" (PDF). Biochimica et Biophysica Acta (BBA) - Specialized Section on Enzymological Subjects. 92 (3): 567–571. doi:10.1016/0926-6569(64)90016-1. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|month=ignored (help) - ^ MIURA, Shoichi (27). "Studies on the Molecular Basis of Development of Serine Dehydratase in Rat Live" (PDF). The Journal of Biochemistry. 4. 68: 543–548. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ ROWSELL, E (1 January 1979). "l-serine dehydratase and l-serine-pyruvate aminotransferase activities in different animal species". Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. 63 (4): 543–555. doi:10.1016/0305-0491(79)90061-0.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ a b Snell, K (1984). "Enzymes of serine metabolism in normal, developing and neoplastic rat tissues". Advances in enzyme regulation. 22: 325–400. PMID 6089514. Retrieved 17 May 2011.
- ^ Harbison, RD (1991). "Hepatic glutathione suppression by the alpha-adrenoreceptor stimulating agents phenylephrine and clonidine" (PDF). Toxicology. 69 (3): 279–90. PMID PMC1683031. Retrieved 17 May 2011.
{{cite journal}}: Check|pmid=value (help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Brämswig, JH (1990 Dec). "Adult height in boys and girls with untreated short stature and constitutional delay of growth and puberty: accuracy of five different methods of height prediction" (PDF). The Journal of pediatrics. 117 (6): 886–91. PMID PMC2246686. Retrieved 17 May 2011.
{{cite journal}}: Check|pmid=value (help); Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ PORTER, P (11 September 1974). "Characterization of human cystathionine β-synthaseEvidence for the identity of human l-serine dehydratase and cystathionine β-synthase" (PDF). Biochimica et Biophysica Acta (BBA) - Enzymology. 364 (1): 128–139. doi:10.1016/0005-2744(74)90140-5. Retrieved 17 May 2011.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ a b Ogawa, Hirofumi (25). "Human Liver Serine Dehydratase" (PDF). T H E J O U R N A L OF BIOLOGICAL CHEMISTRY. 27. 264: 15818–1582. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ CHRISTEN, PHILIPP (16). "From cofactor to enzymes. The molecular evolution of pyridoxal‐5′‐phosphate‐dependent enzymes". The Chemical record. 1 (6): 436. Retrieved 17 May 2011.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help)