Mechanism of Substrate Recognition and PLP-induced Conformational Changes in LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana

Watanabe, Nobuhiko; Clay, Matthew D.; Belkum, Marco J. van; Cherney, M.M.; Vederas, John C.; James, Michael N.G.

doi:10.1016/j.jmb.2008.10.022

Cited by 20 publications

(23 citation statements)

References 32 publications

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“…Therefore, acylation may facilitate the transamination by exposing the keto group at the expense of one succinyl-CoA or acetyl-CoA (15,18,19). However, whether cyclic THDPA is the actual substrate of DapL or DapL catalyzes the ring-opening reaction awaits further investigation (37,38).…”

Section: Resultsmentioning

confidence: 99%

Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis

2010

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The pathway of lysine biosynthesis in the methanococci has not been identified previously. A variant of the diaminopimelic acid (DAP) pathway uses diaminopimelate aminotransferase (DapL) to catalyze the direct conversion of tetrahydrodipicolinate (THDPA) to LL-DAP. Recently, the enzyme DapL (MTH52) was identified in Methanothermobacter thermautotrophicus and shown to belong to the DapL1 group. Although the Methanococcus maripaludis genome lacks a gene that can be unambiguously assigned a DapL function based on sequence similarity, the open reading frame MMP1527 product shares 30% amino acid sequence identity with MTH52. A ⌬mmp1527 deletion mutant was constructed and found to be a lysine auxotroph, suggesting that this DapL homolog in methanococci is required for lysine biosynthesis. In cell extracts of the M. maripaludis wild-type strain, the specific activity of DapL using LL-DAP and ␣-ketoglutarate as substrates was 24.3 ؎ 2.0 nmol min ؊1 mg of protein ؊1 . The gene encoding the DapL homolog in Methanocaldococcus jannaschii (MJ1391) was cloned and expressed in Escherichia coli, and the protein was purified. The maximum activity of MJ1391 was observed at 70°C and pH 8.0 to 9.0. The apparent K m s of MJ1391 for LL-DAP and ␣-ketoglutarate were 82.8 ؎ 10 M and 0.42 ؎ 0.02 mM, respectively. MJ1391 was not able to use succinyl-DAP or acetyl-DAP as a substrate. Phylogenetic analyses suggested that two lateral gene transfers occurred in the DapL genes, one from the archaea to the bacteria in the DapL2 group and one from the bacteria to the archaea in the DapL1 group. These results demonstrated that the DapL pathway is present in marine methanogens belonging to the Methanococcales.

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Section: Resultsmentioning

confidence: 99%

Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis

2010

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“…Recently, several crystal structures of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) have been reported. 14,15 AtDAP-AT is a homodimeric enzyme that belongs to the type I fold family of pyridoxal 5′-phosphate (PLP)-dependent enzymes. 14 Subsequently, the crystal structures of AtDAP-AT in complex with substrates and analogs (e.g., LL-DAP and L-Glu) have provided valuable information on how LL-DAP-AT recognizes those substrates in the active site.…”

Section: Introductionmentioning

confidence: 99%

“…14 Subsequently, the crystal structures of AtDAP-AT in complex with substrates and analogs (e.g., LL-DAP and L-Glu) have provided valuable information on how LL-DAP-AT recognizes those substrates in the active site. 15 As AtDAP-AT and Chlamydia trachomatis LL-DAP-AT (CtDAP-AT) are more than 40% identical in primary sequences ( Supplementary Fig. 1), these studies represent the initial important steps toward the development of inhibitors.…”

Section: Introductionmentioning

confidence: 99%

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The Structure of ll-Diaminopimelate Aminotransferase from Chlamydia trachomatis: Implications for Its Broad Substrate Specificity

Watanabe¹,

Clay²,

Belkum³

et al. 2011

Journal of Molecular Biology

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“…At present, the PDB reports twelve LL-DAP-AT X-ray crystal structures from three species, namely, A. thaliana, C. trachomatis and C. reihardtii (Watanabe et al, 2007(Watanabe et al, , 2008Dobson et al, 2011). The tertiary and quaternary structure of all three proteins are very similar with LL-DAP-AT existing as a homodimer (Fig.…”

Section: Structure Of Ll-dap-atmentioning

confidence: 95%

Enzymology of Bacterial Lysine Biosynthesis

Dogovski¹,

Atkinson²,

Dommaraju³

et al. 2012

Biochemistry

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Mechanism of Substrate Recognition and PLP-induced Conformational Changes in LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana

Cited by 20 publications

References 32 publications

Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis

Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis

The Structure of ll-Diaminopimelate Aminotransferase from Chlamydia trachomatis: Implications for Its Broad Substrate Specificity

Enzymology of Bacterial Lysine Biosynthesis

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