Genome Property Definition Page
| Accession | GenProp0125 | |
| Name | lysine biosynthesis via diaminopimelate (DAP) | |
| Type | METAPATH | |
| Description | The basic amino acid lysine is synthesized in most bacteria and plants via a nine step pathway from aspartate (via aspartate semialdehyde which is also used in a number of other pathways). Most species utilize succinate (from succinyl-CoA) to make an important amide linkage in the ring-opening of piperidine dicarboxylate. The succinate is then hydrolyzed several steps later. Other species carry out analogous transformations with acetate (from acetyl-CoA). Chlamydia and cyanobacteria have been shown to utilize a direct aminotransferase path without the acylation/deacylation steps, and a number of other species apparently also use this variant. Each of these variants are included within this property. A closely related variant (GenProp0788) utilizes the NADPH-dependent enzyme diaminopimelate dehydrogenase (ddh) which incorporates ammonia directly and creates the meso-isomer of diaminopimelate, bypassing the need for the epimerase, DapE. A completely different pathway via alpha-amino adipate exists in fungi and certain bacteria (GenProp0193). Certain obligate intracellular organisms such as Coxiella, Rickettsia and Wolbachia contain all but the final step of this pathway (diaminopimelate decarboxylase). Presumably these organisms have no need of lysine biosynthesis, being able to obtain it from their hosts. The products of the penultimate two steps, however, (LL- and meso-diaminopimelate) are required components of the bacterial cell wall and so the rest of the pathway persists. The formal possibility that the decarboxylase exists in these organsims but is undetected requires that the state of this property remain "some evidence" as opposed to "NO". | |
| JCVI Role | Aspartate family | |
| Parent Property | GenProp0199: lysine biosynthesis | |
| Literature References |
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| Web References | KEGG: Lysine biosynthesis IUBMB: Lysine biosynthesis (early stages) IUBMB: Lysine biosynthesis (later stages) Lysine biosynthesis I:MetaCyc Lysine biosynthesis II:MetaCyc | |
| Gene Ontology Term | GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process) |
Components
| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|---|---|---|---|
| Source of aspartate-semialdehyde | Asp-SA | YES | GenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate | GO:0009089: lysine biosynthetic process via diaminopimelate |
| aminotransferase pathways | BRANCH | NO | GenProp0787 (GENPROP): lysine biosynthesis via diaminopimelate (DAP), acetylated branch GenProp0786 (GENPROP): lysine biosynthesis via diaminopimelate (DAP), succinylated branch TIGR03540 (HMM): LL-diaminopimelate aminotransferase TIGR03542 (HMM): LL-diaminopimelate aminotransferase | GO:0009089: lysine biosynthetic process via diaminopimelate GO:0009089: lysine biosynthetic process via diaminopimelate GO:0009089: lysine biosynthetic process via diaminopimelate GO:0009089: lysine biosynthetic process via diaminopimelate |
| dihydrodipicolinate reductase | DHPR | YES | TIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase TIGR02130 (HMM): dihydrodipicolinate reductase | GO:0009089: lysine biosynthetic process via diaminopimelate GO:0009089: lysine biosynthetic process via diaminopimelate |
| dihydrodipicolinate synthase | DHPS | YES | TIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase | GO:0009089: lysine biosynthetic process via diaminopimelate |
| diaminopimelate epimerase | DapF | YES | TIGR00652 (HMM): diaminopimelate epimerase | GO:0009089: lysine biosynthetic process via diaminopimelate |
| diaminopimelate decarboxylase | LysA | YES | TIGR01048 (HMM): diaminopimelate decarboxylase | GO:0009089: lysine biosynthetic process via diaminopimelate |
Parent Properties
| Accession | Name |
|---|---|
| GenProp0199 | lysine biosynthesis |
Child Properties
| Accession | Name |
|---|---|
| GenProp0786 | lysine biosynthesis via diaminopimelate (DAP), succinylated branch |
| GenProp0787 | lysine biosynthesis via diaminopimelate (DAP), acetylated branch |
Sibling Properties
| Accession | Name |
|---|---|
| GenProp0193 | lysine biosynthesis via alpha-aminoadipate (AAA pathway) |
| GenProp0788 | lysine biosynthesis via diaminopimelate (DAP) utilizing ammonia and NADPH |