Genome Property Definition Page

AccessionGenProp0125
Namelysine biosynthesis via diaminopimelate (DAP)
TypeMETAPATH
DescriptionThe 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 RoleAspartate family
Parent PropertyGenProp0199: lysine biosynthesis
GenProp0199: lysine biosynthesis
GenProp0199: lysine biosynthesis
Literature References
[ 1 ] McCoy AJ, Adams NE, Hudson AO, Gilvarg C, Leustek T, Maurelli AT   L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.   Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17909-14. Epub 2006 Nov 8.  PMID 17093042
[ 1 ] McCoy AJ, Adams NE, Hudson AO, Gilvarg C, Leustek T, Maurelli AT   L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.   Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17909-14. Epub 2006 Nov 8.  PMID 17093042
[ 1 ] McCoy AJ, Adams NE, Hudson AO, Gilvarg C, Leustek T, Maurelli AT   L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.   Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17909-14. Epub 2006 Nov 8.  PMID 17093042
Web ReferencesKEGG: Lysine biosynthesis
IUBMB: Lysine biosynthesis (early stages)
IUBMB: Lysine biosynthesis (later stages)
Lysine biosynthesis I:MetaCyc
Lysine biosynthesis II:MetaCyc
KEGG: Lysine biosynthesis
IUBMB: Lysine biosynthesis (early stages)
IUBMB: Lysine biosynthesis (later stages)
Lysine biosynthesis I:MetaCyc
Lysine biosynthesis II:MetaCyc
KEGG: Lysine biosynthesis
IUBMB: Lysine biosynthesis (early stages)
IUBMB: Lysine biosynthesis (later stages)
Lysine biosynthesis I:MetaCyc
Lysine biosynthesis II:MetaCyc
Gene Ontology TermGO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)
GO:0009089: lysine biosynthetic process via diaminopimelate (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
Source of aspartate-semialdehydeAsp-SAYESGenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
Source of aspartate-semialdehydeAsp-SAYESGenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
Source of aspartate-semialdehydeAsp-SAYESGenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GenProp0160 (GENPROP): aspartate semialdehyde biosynthesis from aspartate
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
aminotransferase pathwaysBRANCHNOGenProp0787 (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 aminotransferaseGenProp0787 (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
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
aminotransferase pathwaysBRANCHNOGenProp0787 (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 aminotransferaseGenProp0787 (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
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
aminotransferase pathwaysBRANCHNOGenProp0787 (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 aminotransferaseGenProp0787 (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
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 reductaseDHPRYESTIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
TIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
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 reductaseDHPRYESTIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
TIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
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 reductaseDHPRYESTIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
TIGR00036 (HMM): 4-hydroxy-tetrahydrodipicolinate reductase
TIGR02130 (HMM): dihydrodipicolinate reductase
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 synthaseDHPSYESTIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
TIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
dihydrodipicolinate synthaseDHPSYESTIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
TIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
dihydrodipicolinate synthaseDHPSYESTIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
TIGR00674 (HMM): 4-hydroxy-tetrahydrodipicolinate synthase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate epimeraseDapFYESTIGR00652 (HMM): diaminopimelate epimerase
TIGR00652 (HMM): diaminopimelate epimerase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate epimeraseDapFYESTIGR00652 (HMM): diaminopimelate epimerase
TIGR00652 (HMM): diaminopimelate epimerase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate epimeraseDapFYESTIGR00652 (HMM): diaminopimelate epimerase
TIGR00652 (HMM): diaminopimelate epimerase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate decarboxylaseLysAYESTIGR01048 (HMM): diaminopimelate decarboxylase
TIGR01048 (HMM): diaminopimelate decarboxylase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate decarboxylaseLysAYESTIGR01048 (HMM): diaminopimelate decarboxylase
TIGR01048 (HMM): diaminopimelate decarboxylase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate
diaminopimelate decarboxylaseLysAYESTIGR01048 (HMM): diaminopimelate decarboxylase
TIGR01048 (HMM): diaminopimelate decarboxylase
GO:0009089: lysine biosynthetic process via diaminopimelate
GO:0009089: lysine biosynthetic process via diaminopimelate

Parent Properties
AccessionName
GenProp0199lysine biosynthesis
GenProp0199lysine biosynthesis
GenProp0199lysine biosynthesis

Child Properties
AccessionName
GenProp0786lysine biosynthesis via diaminopimelate (DAP), succinylated branch
GenProp0787lysine biosynthesis via diaminopimelate (DAP), acetylated branch
GenProp0786lysine biosynthesis via diaminopimelate (DAP), succinylated branch
GenProp0787lysine biosynthesis via diaminopimelate (DAP), acetylated branch
GenProp0786lysine biosynthesis via diaminopimelate (DAP), succinylated branch
GenProp0787lysine biosynthesis via diaminopimelate (DAP), acetylated branch

Sibling Properties
AccessionName
GenProp0193lysine biosynthesis via alpha-aminoadipate (AAA pathway)
GenProp0788lysine biosynthesis via diaminopimelate (DAP) utilizing ammonia and NADPH