Ammonia/Ammonium Reactions

[z-haiman]

Brief description:

Similar to Human-GEM issues #665 and PR#677, all reactions should depend on one form of NH3/NH4+ and have the deprotonation reaction. Human-GEM resolved issue by removing all of the NH4+ versions and keep all of the NH3 version.

Unlike Human-GEM though, sticking with NH4 over NH3 would be preferable.
Reasons for NH4 over NH3:

From Mohiuddin SS, Khattar D. Biochemistry, Ammonia. [Updated 2023 Feb 20]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2024 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK541039/

In nature, ammonia exists as both NH3 and in the ionic form of ammonia as ammonium ion (NH4+). A buffering reaction: NH3+ H+ --> NH4+ is used to maintain the relative amount of each form. Under biological conditions, the pKa of this reaction is about 9.15 and this reaction occurs almost instantaneously. As a result, the majority of ammonia under physiological conditions exists as NH4+, and only about 1.7% of total ammonia presents as NH3 at pH 7.4.

Most physiological scenarios for RBCs will have NH4 prevalent over NH3 due to the pH.

Current status:

Identifier	Reaction equation	Genes
13DAMPPOX	13dampp_c + h2o_c + o2_c --> bamppald_c + h2o2_c + h_c + nh3_c	GAPFILLING
2IMBUTDA	2ibut_c + h2o_c --> 2obut_c + h_c + nh3_c	RIDA
3MOXTYROX	3moxtyr_c + h2o_c + o2_c --> 3mox4hpac_c + h2o2_c + h_c + nh3_c	GAPFILLING
42A12BOOX	dpam__L_c + h2o_c + o2_c --> 34dhpac_c + h2o2_c + h_c + nh3_c	GAPFILLING
CSND	csn_c + h2o_c --> nh3_c + ura_c	GAPFILLING
CTPS1	atp_c + nh3_c + utp_c --> adp_c + ctp_c + h_c + pi_c	CTPS1 or CTPS2
CYTD	cytd_c + h2o_c --> nh3_c + uri_c

Proposed status/to-do list:

Identifier	Reaction equation	Genes
13DAMPPOX	13dampp_c + h2o_c + o2_c --> bamppald_c + h2o2_c + nh4_c	GAPFILLING
2IMBUTDA	2ibut_c + h2o_c --> 2obut_c + nh4_c	RIDA
3MOXTYROX	3moxtyr_c + h2o_c + o2_c --> 3mox4hpac_c + h2o2_c + nh4_c	GAPFILLING
42A12BOOX	dpam__L_c + h2o_c + o2_c --> 34dhpac_c + h2o2_c + nh4_c	GAPFILLING
CSND	csn_c + h2o_c + h_c --> nh4_c + ura_c	GAPFILLING
CTPS1	atp_c + nh4_c + utp_c --> adp_c + ctp_c + 2 h_c + pi_c	CTPS1 or CTPS2
CYTD	cytd_c + h2o_c + h_c --> nh4_c + uri_c
NH4t	nh4_c <=> nh4_e	AQP3 or AQP1 or (RHAG and RHCE and RHD) or (RHAG and RHCE) or RHAG

• Update stoichiometry for 13DAMPPOX.
• Update stoichiometry for 2IMBUTDA.
• Update stoichiometry for 3MOXTYROX.
• Update stoichiometry for 42A12BOOX.
• Update stoichiometry for CSND.
• Update stoichiometry for CTPS1.
• Update stoichiometry for CYTD.
• Add NH4t as reversible transport by RHAG