Carbamoyl phosphate synthetase I

Carbamoyl Phosphate Synthetase I (E.coli: PDB 1jdb, EC 6.3.5.5) is a ligase enzyme located in the mitochondria involved in the production of urea. Carbamoyl Phosphate Synthetase I (CPSI) transfers and ammonia from glutamine to a molecule of bicarbonate that has been phosphorylated by a molecule of ATP. The resulting carbamate is then phosphorylated with another molecule ATP. The resulting molecule of carbamoyl phosphate leaves the enzyme.

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Structure of Carbamoyl Phosphate Synthetase I

CPSI is a heterodimer with a small subunit and a larger subunit with are about 382 and 1073 amino acid residues in size ^[1]. The small subunit contains one active site for the binding and deamination of glutamine to make ammonia and glutamate. The large subunit contains two active sites, one for the production of carboxyphosphate, and the other for the production of carbamoyl phosphate^{[2] [3]}. Within the large subunit there are two domains (B and C) each with an active site of the ATP-grasp family^[1]. Connecting the two subunits a tunnel of sorts which directs the ammonia from the small subunit to the large subunit^[4].

Mechanism of Carbamoyl Phosphate Synthetase I

The overall reaction that occurs in CPSI is:

2ATP + HCO₃^-- + Glutamine --> 2ADP + Carbamoyl phosphate + glutamate + Pi ^[4]

This reaction can be thought of occurring in four distinct steps ^[5].

   1.  Bicarbonate is phosphorylated 
   2.  Ammonia is taken off glutamine
   3.  The ammonia from glutamine attacks the carboxyphosphate resulting in carbamate
   4.  Carbamate is phosphorylated to give Carbamoyl phosphate

Of these four steps only step two, the deamination of glutamine to get ammonia is known to have actively participating amino acid residues, Cys269 and His353. The other three steps mostly utilize amino acid residue to form hydrogen bonds with substrates. A video of a simplified version of this mechanism is available here

Recent Mechanism Studies

It has been found that both ATP-binding sites in the large subunit of CPSI are structurally equivalent. A recent study has investigated the interlinking between these two domains (domain B and domain C) and has found evidence that they are coupled. This ATP-binding domain coupling works such that a molecule of ATP binding at one site (domain C) conformationally allows synthesis at the other domain (domain B). If this turns out to be true then the mechanism for carbamoyl phosphate synthesis is significantly altered. Instead of forming carbamoyl phosphate in step 5 (of the included mechanism below) by ejecting ADP it would be formed at step 4 by protonating the alcohol group and then kicking it off as water.^[6].

Regulation

CPSI is allosterically regulated by purine and pyrimidine nucleotides where the former is allosterically activates the enzyme and the later allosterically inhibits CPSI. Also, it has been found that ornithine is a allosteric activator of CPSI. Increased levels of ammonia also activate CPSI while decreased levels of ATP inhibit CPSI activity. All allosteric binding sites are located in the large subunit of the enzyme ^[5].

Carbamoyl Phosphate Synthetase I and Metabolism

CPSI plays a vital role in protein and nitrogen metabolism. Once ammonia has been brought into the mitochondria via glutamine, or glutamate it is CPSI’s job to add the ammonia to bicarbonate along with a phosphate group to form carbamoyl phosphate. Carbamoyl phosphate is then put into the urea cycle to eventually create urea. Urea can then be transferred back to the blood stream and to the kidneys for filtration and on to the bladder for excretion^[8].

Health Problems related to Carbamoyl Phosphate Synthetase I

The main problem related to CPSI is genetically based. Sometimes the body doesn’t produce enough CPSI due to a mutation in the genetic code. When this happens the body can’t metabolize proteins and nitrogen as well and this can result in high levels of ammonia in the body. This is dangerous because ammonia is highly toxic to the body and especially the nervous system and can result in retardation and seizures. For more information check out the article on Carbamoyl phosphate synthetase I deficiency.

References

1. ^ ^{a b} James B. Thoden‡, Xinyi Hua, et al. “Carbamoyl-phosphate Synthetase: Creation of an Escape Route for Ammonia.” From the ‡Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706-1544 and the §Department of Chemistry, Texas A&M University, College Station, Texas 77843-3012. http://www.jbc.org/cgi/reprint/277/42/39722.pdf
2. ^ SUE GLENN POWERS, “Inhibition of Carbamyl Phosphate Synthetase by PI, P5-Di(adenosine 5’)- pentaphosphate EVIDENCE FOR TWO ATP BINDING SITES.” From the Department ofBiochemistry, Cornell University Medical College, New York, New York 10021. http://www.jbc.org/cgi/reprint/252/10/3558
3. ^ James B. Thoden, Hazel M. Holden, et al (1997). “Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 Å from Substrate to Product.” Institute for Enzyme Research, Graduate School, and Department of Biochemistry, College of Agriculture, UniVersity of Wisconsin, Madison, Wisconsin 53705, and Department of Chemistry, Texas A&M UniVersity, College Station, Texas 77843. http://pubs.acs.org/cgi-bin/article.cgi/bichaw/1997/36/i21/pdf/bi970503q.pdf
4. ^ ^{a b} Jungwook Kim and Frank M. Raushel (2004). “Perforation of the Tunnel Wall in Carbamoyl Phosphate Synthetase Derails the Passage of Ammonia between Sequential Active Sites.” Department of Chemistry, Texas A&M UniVersity, P.O. Box 30012, College Station, Texas 77842-3012. http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2004/43/i18/pdf/bi049945+.pdf
5. ^ ^{a b} ALTON MEISTER. “MECHANISM AND REGULATION OF THE GLUTAMINE-DEPENDENT CARBAMYL PHOSPHATE SYNTHETASE OF ESCHERZCHZA COLI.” Department of Biochemistry, Cornell University Medical College, New York, New York 10021
6. ^ MICHAEL KOTH*, BINNUR EROGLU, et al. “Novel mechanism for carbamoyl-phosphate synthetase: A nucleotide switch for functionally equivalent domains.” Department of Biology, Northeastern University, Boston, MA 02115 http://www.pnas.org/cgi/reprint/94/23/12348.pdf?ck=nck
7. ^ James B. Thoden, et al (1998). “Carbamoyl Phosphate Synthetase: Caught in the Act of Glutamine Hydrolysis.” Biochemistry 1998, 37, 8825-8831. http://pubs.acs.org/cgi-bin/article.cgi/bichaw/1998/37/i25/pdf/bi9807761.pdf
8. ^ David Nelson and Michael Cox. “Principles of Biochemistry, fourth edition.” Pgs 666-669