Duplicate Beta-Oxidation Reactions for Pristanoyl-CoA

[Devlin-Moyer]

Some of these changes depend on the ones proposed in #776

Current behavior:

There are two parallel pathways representing the peroxisomal beta-oxidation of 4,8,12-trimethyltridecanoyl-CoA to 4,8-dimethylnonanoyl-CoA:

ID	Reaction	Notes
MAR03506	4,8,12-trimethyltridecanoyl-CoA [x] + FAD [x] --> (4R,8R,12R)-trimethyl-(2E)-tridecenoyl-CoA [x] + FADH2 [x]
MAR03508	(4R,8R,12R)-trimethyl-(2E)-tridecenoyl-CoA [x] + H2O [x] --> 3(R)-hydroxy-(4R,8R,12R)-trimethyl-tridecanoyl-CoA [x]
MAR03509	3(R)-hydroxy-(4R,8R,12R)-trimethyl-tridecanoyl-CoA [x] + NAD+ [x] --> 3-oxo-(4R,8R,12R)-trimethyl-tridecanoyl-CoA [x] + H+ [x] + NADH [x]
MAR03510	3-oxo-(4R,8R,12R)-trimethyl-tridecanoyl-CoA [x] + CoA [x] --> (2R,6R,10R)-trimethyl-hendecanoyl-CoA [x] + acetyl-CoA [x]
MAR05108	4,8,12-trimethyltridecanoyl-CoA [x] + CoA [x] + FAD [x] + H2O [x] + NAD+ [x] --> acetyl-CoA [x] + FADH2 [x] + H+ [x] + NADH [x] + 2,6,10-Trimethyl Undecanoyl Coenzyme A [x]	Redundant with MAR03506 through MAR03510
MAR03511	(2R,6R,10R)-trimethyl-hendecanoyl-CoA [x] --> (2S,6R,10R)-trimethyl-hendecanoyl-CoA [x]
MAR03512	(2S,6R,10R)-trimethyl-hendecanoyl-CoA [x] + FAD [x] --> (2S,6R,10R)-trimethyl-(2E)-hendecenoyl-CoA [x] + FADH2 [x]
MAR03513	(2S,6R,10R)-trimethyl-(2E)-hendecenoyl-CoA [x] + H2O [x] --> 3(R)-hydroxy-(2S,6R,10)-trimethyl-hendecanoyl-CoA [x]
MAR03514	3(R)-hydroxy-(2S,6R,10)-trimethyl-hendecanoyl-CoA [x] + NAD+ [x] --> 3-oxo-(2S,6R,10R)-trimethyl-hendecanoyl-CoA [x] + H+ [x] + NADH [x]
MAR03515	3-oxo-(2S,6R,10R)-trimethyl-hendecanoyl-CoA [x] + CoA [x] --> 4(R),8-dimethyl-nonanoyl-CoA [x] + propanoyl-CoA [x]
MAR05028	CoA [x] + FAD [x] + H2O [x] + NAD+ [x] + 2,6,10-Trimethyl Undecanoyl Coenzyme A [x] --> FADH2 [x] + H+ [x] + NADH [x] + propanoyl-CoA [x] + 4,8-Dimethylnonanoyl Coenzyme A [x]	Redundant with MAR03511 through MAR03515
MAR00139	L-carnitine [x] + 4,8-Dimethylnonanoyl Coenzyme A [x] <=> 4,8-dimethylnonanoylcarnitine [x] + CoA [x]	Should only have CROT in its GPR, not also CRAT (sources: 1, 2)
MAR04782	4,8-dimethylnonanoylcarnitine [x] <=> 4,8-dimethylnonanoylcarnitine [c]	Should not be associated with SLC25A20
MAR03521	4(R),8-dimethyl-nonanoyl-CoA [c] + L-carnitine [c] <=> 4,8-dimethylnonanoylcarnitine [c] + CoA [c]
MAR03517	4(R),8-dimethyl-nonanoyl-CoA [c] <=> 4(R),8-dimethyl-nonanoyl-CoA [x]	Less realistic version of MAR00139 + MAR04782 + MAR03521 (source)
MAR03520	4,8-dimethylnonanoylcarnitine [c] + L-carnitine [m] <=> 4,8-dimethylnonanoylcarnitine [m] + L-carnitine [c]	GPR should be SLC25A20 (currently empty)
MAR00315	4,8-dimethylnonanoylcarnitine [c] <=> 4,8-dimethylnonanoylcarnitine [m]	Less accurate version of MAR03520
MAR00138	4,8-dimethylnonanoylcarnitine [x] <=> 4,8-dimethylnonanoylcarnitine [m]	Duplicate of MAR00139 + MAR00315

I know that removing SLC25A20 from the GPR of MAR04782 would leave it without a GPR, but as far as I can tell, people are confident that SLC25A20 is not in peroxisomal membranes, and some other as yet unidentified protein is responsible for transporting acylcarnitines out of peroxisomes (see e.g. this paper).

Proposed changes:

• Remove MAR05108 for being a duplicate of MAR03506 + MAR03508 + MAR03509 + MAR03510
• Remove MAR05028 for being a duplicate of MAR03512 + MAR03513 + MAR03514 + MAR03515
• Remove MAM04004x for being a duplicate of MAM00076x and MAM00080x
• Replace MAM03554x with MAM00933x in MAR00139
• Remove MAM03554x for being a duplicate of MAM00933x
• Remove ENSG00000095321 from GPR of MAR00139
• Remove ENSG00000178537 from GPR of MAR04782
• Add ENSG00000178537 to GPR of MAR03520
• Remove MAR00318 for being a duplicate of MAR00139 + MAR00315