Carbamoyl phosphate synthetase III

Carbamoyl phosphate synthetase III (CPS III) is one of the three isoforms of the carbamoyl phosphate synthetase, an enzyme that catalyzes the active production of carbamoyl phosphate in many organisms.

CPS III (EC 6.3.5.5.) is a ligase (3.) that forms carbon-nitrogen bonds (6.3.) with glutamine as amido-N-donor (6.3.5.) (see BRENDA).

Context

Many aquatic organisms, including most of the fish species, are ammoniotelic, which means they produce ammonia as metabolic waste, that they generally excrete by diffusion through their gills. Similar to terrestrial vertebrates, some fish species also significantly include urea as metabolic waste. This phenomenon concerns larvae stages since they do not have gills to excrete ammonia from, but also the adult stage in some species. Based on the proportion of metabolic waste represented by urea, these species are partial or fully ureotelic.

Ureotelic species produce urea via the ornithine-urea cycle (OUC) in which CPS plays an important role. Carbamoyl phosphate synthetase I is mostly used by terrestrial vertebrates, and it appears that some aquatic species rely on CPS III to deal with urea production.[1] There are several potential advantages in excreting urea instead of ammonia for species living in specific environments. For example, it allows a better diffusion capacity than ammonia in alkaline waters,[2] and it decreases water loss, which can be crucial for species experiencing long periods out of the water such as lungfish species.[3] CPS III has been described in cichlids of the Alcolapia genus,[2] lungfishes,[3][4][5] the gulf toadfish Opsanus beta,[6] the rainbow trout Oncorhyncus mykiss,[7][8] the Atlantic halibut Hippoglossus hippoglossus,[9] the largemouth bass Micropterus salmoides,[10] the common carp Cyprinus carpio,[11] and in elasmobranchs such as the spiny dogfish Squalus acanthia[12][13] for example. This enzyme thus seems to be distributed among fish showing different degree of ureotely.

Reaction pathway

Ornithine-urea cycle

CPS III is a precursor in the ornithine-urea cycle (OUC). This pathway occurs in organisms which do not directly excrete ammonia as a catabolic waste. The main function of the OUC is to convert highly toxic nitrogen waste (NH3) in urea, which shows less toxicity. This cycle includes five biochemical reactions, the first two of which occur in the mitochondrial matrix and the three others in the cytosol. In fishes, the urea cycle is only found in a few teleosts, mostly air breeders or species living in very specific environments such as alkaline water,[14] and in elasmobranchs.

CPS III is found in the mitochondria of some elasmobranch and in a few teleosts liver and/or extrahepatic tissues. It intervenes in the first reaction of the cycle of the OUC, which is crucial since it limits the rest of the cycle. CPS III thus plays a major role in regulating the amount of ammonia in the cell, by starting its conversion in urea for excretion while maintaining a minimum concentration to maintain amino acids synthesis.

Carbamoyl phosphate synthesis

The reaction catalyzed by CPS III is:[15] 2 ATP + L-glutamine + HCO3- + H20 → 2 ADP + Pi + L-glutamate + carbamoyl phosphat

This reaction occurs in the mitochondrial matrix and include 4 steps:          

  1. Bicarbonate (HCO3−) is phosphorylated using an ATP, generating carboxyphosphate (CHO6P2-)
  2. Glutamine (C5H10N2O3) is hydrolyzed into glutamate (C5H9NO4) and ammonia (NH3). 1. and 2. occur concurrently.
  3. Nucleophilic substitution of the ammonia on carboxyphosphate (substituting the -OH group by a -NH2 group) generating the intermediate product carbamate (CH2NO2−)
  4. Nucleophilic substitution of the carbamate on a second ATP, generating the product carbamoyl phosphate (CH
    2    NO
    5    P2−
    ).

CPS III, like CPS I, shows a N-acetylglutamate-dependent, which means that this allosteric effector is required to perform the catalysis.[4]

Structure

CPS III is composed of two subunits: a synthetase and a glutaminase. These two subunits seem to be fused by the N-terminal end of the synthetase[16] (Hong et al., 1994)

The 38 first amino acids of the sequence (N-terminal sequence) represent a mitochondrial signal sequence to signal import in the mitochondria.

The glutaminase subunit is located between Phe39 and Ile407 and is itself divided into two domains: an N-terminal domain between Phe39 and Asp165, and a C-terminal glutamine amide transferase domain (GAT) located between Thr166 and Ile407. The cysteine residue Cyst294 along with three histidine residues Hist337, Hist367, and Hist378, have been identified as crucial for the glutamine-dependent activity. In other words, these residues allow CPS III to use glutamine as a substrate.

The synthetase subunit stretches from Lys425 to Gln15032 (C-terminal end) and is also composed of two domains. The first one is located between Lys425 and Ile977 and the second one between Met978 and Gln1502. Each may contain an ATP binding site located between Arg719 and Asp768, and between Arg1260 and Ile1304. It is believed that the C-terminal region contains the binding site for the fixation of the allosteric effector N-acetylglutamate (NAG) which is required for CPS III to function. Two cysteines Cys1328 and Cys1338 have been identified in CPS I, which also use NAG as an allosteric effector, but not in CPS II, which activity is not affected by NAG. Thus, these two cysteine residues appear to probably play a crucial role in the allosteric activity of CPS III.

Evolution and relationship with CPS I and CPS II

CPS III is closer to CPS I than CPS II.[16] These two enzymes work the same way and use the same allosteric effector. The difference between them is that CPS III uses glutamine as substrate while CPS I use ammonia.

It is believed that these enzymes evolved from each other. One hypothesis is that CPS II appeared first after the fusion of genes coding for a glutaminase and an ammonia-dependent synthetase. CPS III would then result from the duplication of the glutaminase sequence, creating a second glutamine binding site that evolved into the N-acetylglutamate allosteric site. The last type, CPS I would be the last one to appear after evolving in using ammonia as substrate instead of glutamine.[17][4][18]

References
  1. Anderson PM (January 1995). Wood CM, Shuttleworth TJ (eds.). "3 Urea Cycle in Fish: Molecular and Mitochondrial Studies". Fish Physiology. Academic Press. 14: 57–83. doi:10.1016/s1546-5098(08)60242-3. ISBN 9780123504388.
  2. White LJ, Sutton G, Shechonge A, Day JJ, Dasmahapatra KK, Pownall ME (October 2020). "Adaptation of the carbamoyl-phosphate synthetase enzyme in an extremophile fish". Royal Society Open Science. 7 (10): 201200. Bibcode:2020RSOS....701200W. doi:10.1098/rsos.201200. PMC 7657897. PMID 33204476.
  3. Chew SF, Ong TF, Ho L, Tam WL, Loong AM, Hiong KC, et al. (October 2003). "Urea synthesis in the African lungfish Protopterus dolloi--hepatic carbamoyl phosphate synthetase III and glutamine synthetase are upregulated by 6 days of aerial exposure". The Journal of Experimental Biology. 206 (Pt 20): 3615–24. doi:10.1242/jeb.00619. PMID 12966053. S2CID 9687376.
  4. Laberge T, Walsh PJ (June 2011). "Phylogenetic aspects of carbamoyl phosphate synthetase in lungfish: a transitional enzyme in transitional fishes". Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. 6 (2): 187–94. doi:10.1016/j.cbd.2011.03.001. PMID 21482211.
  5. Loong AM, Chng YR, Chew SF, Wong WP, Ip YK (April 2012). "Molecular characterization and mRNA expression of carbamoyl phosphate synthetase III in the liver of the African lungfish, Protopterus annectens, during aestivation or exposure to ammonia". Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology. 182 (3): 367–79. doi:10.1007/s00360-011-0626-7. PMID 22038021. S2CID 6766714.
  6. Kong H, Kahatapitiya N, Kingsley K, Salo WL, Anderson PM, Wang YS, Walsh PJ (January 2000). "Induction of carbamoyl phosphate synthetase III and glutamine synthetase mRNA during confinement stress in gulf toadfish (Opsanus beta)". The Journal of Experimental Biology. 203 (Pt 2): 311–20. doi:10.1242/jeb.203.2.311. PMID 10607541.
  7. Korte JJ, Salo WL, Cabrera VM, Wright PA, Felskie AK, Anderson PM (March 1997). "Expression of carbamoyl-phosphate synthetase III mRNA during the early stages of development and in muscle of adult rainbow trout (Oncorhynchus mykiss)". The Journal of Biological Chemistry. 272 (10): 6270–7. doi:10.1074/jbc.272.10.6270. PMID 9045644.
  8. Todgham AE, Anderson PM, Wright PA (June 2001). "Effects of exercise on nitrogen excretion, carbamoyl phosphate synthetase III activity and related urea cycle enzymes in muscle and liver tissues of juvenile rainbow trout (Oncorhynchus mykiss)". Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology. 129 (2–3): 527–39. doi:10.1016/S1095-6433(01)00290-2. PMID 11423323.
  9. Terjesen BF, Rønnestad I, Norberg B, Anderson PM (August 2000). "Detection and basic properties of carbamoyl phosphate synthetase III during teleost ontogeny: a case study in the Atlantic halibut (Hippoglossus hippoglossus L.)". Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 126 (4): 521–35. doi:10.1016/S0305-0491(00)00221-2. PMID 11026664.
  10. Kong H, Edberg DD, Korte JJ, Salo WL, Wright PA, Anderson PM (February 1998). "Nitrogen excretion and expression of carbamoyl-phosphate synthetase III activity and mRNA in extrahepatic tissues of largemouth bass (Micropterus salmoides)". Archives of Biochemistry and Biophysics. 350 (2): 157–68. doi:10.1006/abbi.1997.0522. PMID 9473289.
  11. Felskie AK, Anderson PM, Wright PA (1998-02-01). "Expression and Activity of Carbamoyl Phosphate Synthetase III and Ornithine Urea Cycle Enzymes in Various Tissues of Four Fish Species". Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 119 (2): 355–364. doi:10.1016/S0305-0491(97)00361-1. ISSN 1096-4959.
  12. Hong J, Salo WL, Chen Y, Atkinson BG, Anderson PM (December 1996). "The promoter region of the carbamoyl-phosphate synthetase III gene of Squalus acanthias". Journal of Molecular Evolution. 43 (6): 602–9. Bibcode:1996JMolE..43..602H. doi:10.1007/BF02202108. PMID 8995057. S2CID 6835045.
  13. Chana-Munoz A, Jendroszek A, Sønnichsen M, Kristiansen R, Jensen JK, Andreasen PA, et al. (2017-08-23). "Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation". PLOS ONE. 12 (8): e0182756. Bibcode:2017PLoSO..1282756C. doi:10.1371/journal.pone.0182756. PMC 5568229. PMID 28832628.
  14. Randall DJ, Wood CM, Perry SF, Bergman H, Maloiy GM, Mommsen TP, Wright PA (January 1989). "Urea excretion as a strategy for survival in a fish living in a very alkaline environment". Nature. 337 (6203): 165–6. Bibcode:1989Natur.337..165R. doi:10.1038/337165a0. PMID 2911349. S2CID 4272256.
  15. Holden HM, Thoden JB, Raushel FM (October 1999). "Carbamoyl phosphate synthetase: an amazing biochemical odyssey from substrate to product". Cellular and Molecular Life Sciences. 56 (5–6): 507–22. doi:10.1007/s000180050448. PMID 11212301. S2CID 23446378.
  16. Hong J, Salo WL, Lusty CJ, Anderson PM (October 1994). "Carbamyl phosphate synthetase III, an evolutionary intermediate in the transition between glutamine-dependent and ammonia-dependent carbamyl phosphate synthetases". Journal of Molecular Biology. 243 (1): 131–40. doi:10.1006/jmbi.1994.1638. PMID 7932737.
  17. Devaney MA, Powers-Lee SG (January 1984). "Immunological cross-reactivity between carbamyl phosphate synthetases I, II, and III". The Journal of Biological Chemistry. 259 (2): 703–6. doi:10.1016/S0021-9258(17)43514-9. PMID 6363405.
  18. Lindley TE, Laberge T, Hall A, Hewett-Emmett D, Walsh PJ, Anderson PM (March 2007). "Sequence, expression and evolutionary relationships of carbamoyl phosphate synthetase I in the toad Xenopus laevis". Journal of Experimental Zoology Part A: Ecological Genetics and Physiology. 307 (3): 163–75. doi:10.1002/jez.a.364. PMID 17397070.
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