Subsystem: D-galactarate, D-glucarate and D-glycerate catabolism - gjo

This subsystem's description is:

Variant codes:

1 No Glucarate/Galactorate utilization. Glycerate is utilized by GK+glyT.
2 B.subtilis-like Glucarate/Galactorate utilization via GT(optional)+GD+kdgD
3. E.coli-like Glucarate/Galactorate utilization via GT(optional)+GD+garL+garR+GK.
4. Combination of 1 and 2 variants.
5. Combination of 2 and 3 variants.
6. Combination of 1 and 3 variants.

-1 No Glucarate/Galactorate or Glycerate utilization

For more information, please check out the description and the additional notes tabs, below

DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

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Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature
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Taxonomy Pattern 
Organism 
Domain
Variant [?] 
active
GK1GlyTSdaRGarPGarDGudPGudDGudD_XGudD_X2GarRGarLKdgDGK2YcbGGR_GntRGR_IclRGK2_X
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Variant codes:

1 No Glucarate/Galactorate utilization. Glycerate is utilized by GK+glyT.
2 B.subtilis-like Glucarate/Galactorate utilization via GT(optional)+GD+kdgD
3. E.coli-like Glucarate/Galactorate utilization via GT(optional)+GD+garL+garR+GK.
4. Combination of 1 and 2 variants.
5. Combination of 2 and 3 variants.
6. Combination of 1 and 3 variants.

-1 No Glucarate/Galactorate or Glycerate utilization
Catabolism of D-Glycerate (three-carbon acid), D-galactarate and D-glucarate (sugar hexos es diacids)

Glucarate and galactarate are utilized by homologous permeases (GarP and GudP) and dehydratases (GarD and GudD), both producing 5-dehydro-4-deoxyglucarate (or 2-dehydro-3-deoxyglucarate in other nomenclature). There are two different routes to catabolize 5-dehydro-4-deoxyglucarate:
1. As in E.coli: The GarL aldolase splits it to pyruvate and tartronate semialdehyde, and the latter is reduced by the GarR reductase, phosphorylated by GarK kinase to produce 2-phosphoglycerate, an intermediate of Glycolysis.
2. as in B.subtilis: The 5-dehydro-4-deoxyglucarate dehydratase (decarboxylating), or KdgD, produces 2,5-dioxopentanoate which is then metabolized to 2-oxoglutarate by a common dehydrogenase.

Many species lack D-galactarate and D-glucarate utilization genes but have only D-glycerate kinase in a cluster with predicted D-glycerate transporter (a homolog of the gluconate permease GntP), and with the sugar diacid regulator sdaR.

Sugar diacid regulator SdaR was characterized only in E.coli, where it co-regulates genes D-galactarate and D-glucarate catabolism and where D-glycerate transporter is missed. However it seems that SdaR senses D-glycerate, a common intermediate of D-galactarate and D-glucarate catabolism. In many other Gram-negative and Gram-positive species SdaR was found in a cluster with D-glycerate kinase and transporter, thus confirming that it sence D-glycerate.

In some taxonomic groups D-galactarate and D-glucarate utilization clusters contains a conserved transcriptional regulators from either GntR or IclR family, and we suggest them as a specific regulators of these pathways.

GarR reductase converting tartronate semialdehyde to D-glycerate is more common and may be involved in other metabolic pathways like Allantoin and purines catabolism, tartrate catabolism and others.
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Based on the system of Rodionov, but noting that D-glycerate kinase phosphorylates the 2 position.