Omega-amidase

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Omega-amidase
Omega-Amidase.png
A 3D cartoon depiction of the crystal structure of mouse nitrilase 2.
Identifiers
EC number3.5.1.3
CAS number9025-19-8
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO

In enzymology, an omega-amidase (EC 3.5.1.3) is an enzyme that catalyzes the chemical reaction

a monoamide of a dicarboxylic acid + H2O a dicarboxylate + NH3

Thus, the two substrates of this enzyme are monoamide of a dicarboxylic acid and H2O, whereas its two products are dicarboxylate and NH3.

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is omega-amidodicarboxylate amidohydrolase. This enzyme is also called alpha-keto acid-omega-amidase. This enzyme participates in glutamate metabolism and alanine and aspartate metabolism. This enzyme can be found in mammals, plants, and bacteria.[1]

Structure and active site[edit]

Omega-amidase has two independent monomers that have structure organizations similar to other nitrilase enzymes found in bacteria.[2] Each monomer has a four layered alpha/beta/beta/alpha conformation.[2] The enzyme is asymmetrical and contains a carbon-nitrogen hydrolase fold.[2]

Theoretical active site based on the proximity of residues of the catalytic triad.[3]

Just as omega-amidase shares a general structure organization as other nitrilases, omega-amidase also contains the same catalytic triad within the active site. This triad of residues includes a nucleophilic cysteine, a glutamate base, and a lysine, all of which are conserved within the structure.[2] In addition to the catalytic triad, omega-amidase also contains a second glutamate that assists in substrate positioning.[3] This second glutamate is why omega-amidase has no activity with glutamine or asparagine, even though they are sized similarly to typical substrates.[4]

Mechanism[edit]

Omega amidase catalyzes the deamidation of several different alpha-keto acids into ammonia and metabolically useful carboxylic acids[5] The general mechanism is the same as for other nitrilases: binding of the substrate to the active site, followed by release of ammonia, formation of a thioester intermediate at the cysteine, binding of water and then release of the carboxylic acid product.[3] Specifically, the active site cysteine acts as a nucleophile and binds to the substrate.[6] The catalytic triad glutamate transfers a proton to the amide group to create and release ammonia.[7] The remaining thioester intermediate is stabilized by the lysine and the backbone amino group following the cysteine.[6] This intermediate is attacked by water to form a stable tetrahedral intermediate.[7] This intermediate breaks down to release the carboxylic acid and restore the enzyme.[7]

Biology[edit]

Omega-amidase operates in coordination with glutamine transaminase to finish off the methionine salvage cycle in bacteria and plants.[1] In the last step to obtain methionine from α-ketomethylthiobutyrate(KMTB), glutamine transaminase K(GTK) converts glutamine to α-ketoglutaramate(KGM).[1] KGM is the main substrate for omega amidase, but KGM exists mainly in the ring form at physiological conditions.[4] Omega-amidase has a higher affinity for the open linear form of KGM that forms more readily at pH 8.5.[8] GTK catalyzes a reversible reaction, but coupling it with omega-amidase makes the transamination reaction irreversible at physiological conditions.[8]

Due to omega-amidase's ability to convert toxic substrates like KGM into components that can be used by other processes, this enzyme can be considered a repair enzyme.[9] Some such substrates are linked to diseases or conditions such as hyperammonemia.[10] A list of some of the substrates that omega-amidase catalyzes may be found in Table 1.  

Table 1. Substrate/Product pairs catalyzed by omega-amidase
Substrate Product
α-Ketoglutaramate α-Ketoglutamate
α-Ketosuccinamate Oxaloacetate
L-2-Hydroxysuccinamate L-Malate
Succinamic Acid Succinylmonohydroxamic Acid[11]
Glutaramic Acid Glutarylmonohyoxamic Acid[11]

Medical relevance[edit]

The NIT2 gene in humans has been found to be identical to omega-amidase.[9] The gene has the highest expression in the liver and kidney, but is also expressed in almost every human tissue.[5] Overexpression of the NIT2 gene results in decreasing cell proliferation and growth in HeLa cells, which indicates that the gene may have a role in tumor suppression.[9] However further studies are necessary to determine the effect on specific cancers, as a study done with colon cancer cells showed that downregulation of NIT2 induced cell cycle arrest.[12] In addition to tumor suppression, NIT2/omega-amidase may be useful for detection and conversion of oncometabolites.[13] Because omega-amidase is able to control concentration of toxic substrates such as KGM, it is likely that NIT2 can serve the same purpose.[13]

References[edit]

  1. ^ a b c Ellens KW, Richardson LG, Frelin O, Collins J, Ribeiro CL, Hsieh YF, Mullen RT, Hanson AD (May 2015). "Evidence that glutamine transaminase and omega-amidase potentially act in tandem to close the methionine salvage cycle in bacteria and plants". Phytochemistry. 113: 160–9. doi:10.1016/j.phytochem.2014.04.012. PMID 24837359.
  2. ^ a b c d Barglow KT, Saikatendu KS, Bracey MH, Huey R, Morris GM, Olson AJ, Stevens RC, Cravatt BF (December 2008). "Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes". Biochemistry. 47 (51): 13514–23. doi:10.1021/bi801786y. PMC 2665915. PMID 19053248.
  3. ^ a b c Weber BW, Kimani SW, Varsani A, Cowan DA, Hunter R, Venter GA, Gumbart JC, Sewell BT (October 2013). "The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning". The Journal of Biological Chemistry. 288 (40): 28514–23. doi:10.1074/jbc.m113.503284. PMC 3789952. PMID 23946488.
  4. ^ a b Chien CH, Gao QZ, Cooper AJ, Lyu JH, Sheu SY (July 2012). "Structural insights into the catalytic active site and activity of human Nit2/ω-amidase: kinetic assay and molecular dynamics simulation". The Journal of Biological Chemistry. 287 (31): 25715–26. doi:10.1074/jbc.m111.259119. PMC 3406660. PMID 22674578.
  5. ^ a b Krasnikov BF, Nostramo R, Pinto JT, Cooper AJ (August 2009). "Assay and purification of omega-amidase/Nit2, a ubiquitously expressed putative tumor suppressor, that catalyzes the deamidation of the alpha-keto acid analogues of glutamine and asparagine". Analytical Biochemistry. 391 (2): 144–50. doi:10.1016/j.ab.2009.05.025. PMC 2752201. PMID 19464248.
  6. ^ a b Stevenson DE, Feng R, Storer AC (December 1990). "Detection of covalent enzyme-substrate complexes of nitrilase by ion-spray mass spectroscopy". FEBS Letters. 277 (1–2): 112–4. doi:10.1016/0014-5793(90)80821-y. PMID 2269339.
  7. ^ a b c Thuku RN, Brady D, Benedik MJ, Sewell BT (March 2009). "Microbial nitrilases: versatile, spiral forming, industrial enzymes". Journal of Applied Microbiology. 106 (3): 703–27. doi:10.1111/j.1365-2672.2008.03941.x. PMID 19040702.
  8. ^ a b Zhang Q, Marsolais F (March 2014). "Identification and characterization of omega-amidase as an enzyme metabolically linked to asparagine transamination in Arabidopsis". Phytochemistry. 99: 36–43. doi:10.1016/j.phytochem.2013.12.020. PMID 24461228.
  9. ^ a b c Huebner K, Saldivar JC, Sun J, Shibata H, Druck T (2011). "Hits, Fhits and Nits: beyond enzymatic function". Advances in Enzyme Regulation. 51 (1): 208–17. doi:10.1016/j.advenzreg.2010.09.003. PMC 3041834. PMID 21035495.
  10. ^ Krasnikov BF, Deryabina YI, Isakova EP, Biriukova IK, Shevelev AB, Antipov AN (May 2017). "New recombinant producer of human ω-amidase based on Escherichia coli". Applied Biochemistry and Microbiology. 53 (3): 290–295. doi:10.1134/s0003683817030115.
  11. ^ a b Meister A, Levintow L, Greenfield RE, Abendschein PA (July 1955). "Hydrolysis and transfer reactions catalyzed by omega-amidase preparations". The Journal of Biological Chemistry. 215 (1): 441–60. PMID 14392177.
  12. ^ Zheng B, Chai R, Yu X (May 2015). "Downregulation of NIT2 inhibits colon cancer cell proliferation and induces cell cycle arrest through the caspase-3 and PARP pathways". International Journal of Molecular Medicine. 35 (5): 1317–22. doi:10.3892/ijmm.2015.2125. PMID 25738796.
  13. ^ a b Hariharan VA, Denton TT, Paraszcszak S, McEvoy K, Jeitner TM, Krasnikov BF, Cooper AJ (March 2017). "The Enzymology of 2-Hydroxyglutarate, 2-Hydroxyglutaramate and 2-Hydroxysuccinamate and Their Relationship to Oncometabolites". Biology. 6 (2): 24. doi:10.3390/biology6020024. PMID 28358347.

Further reading[edit]

  • Meister A, Radhakrishnan AN, Buckley SD (December 1957). "Enzymatic synthesis of L-pipecolic acid and L-proline". The Journal of Biological Chemistry. 229 (2): 789–800. PMID 13502341.