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B6db activities: 4.1.1.20

4.1.1.20
Description Diaminopimelate decarboxylase
Alternative names meso-diaminopimelate decarboxylase;
meso-diaminopimelic acid decarboxylase;
DAP decarboxylase;
DAPDC.
Catalyzed reaction Meso-2,6-diaminoheptanedioate = L-lysine + CO(2).
Cofactor Pyridoxal-phosphate.
Comments Bacteria have developed at least three different routes to synthesize lysine from aspartate, but in each of these routes lysine is ultimately produced by decarboxylating diaminopimelate (DAP), a metabolite that is also involved in peptidoglycan formation.

DAP is a symmetric molecule, containing two alpha carbons - one in configuration L, the other in configuration D. The enzyme selectively removes the carboxylate group from the latter, to generate L-lysine.
Thus, diaminopimelate decarboxylase is a rare case of PLP-dependent D-amino-acid decarboxylase, together with the strictly related D-ornithine/D-lysine decarboxylase (4.1.1.116).

Prosite PROSITE; PDOC00685;
PDB 1HKW; 1TWI; 5X7M;
Organisms -Eubacteria -Archea -Plants
 

Family 

4.1.1.20 (43)
 
Links Enzyme (activities) 4.1.1.20
BRENDA (activities) 4.1.1.20
KEGG (pathways) 4.1.1.20
PLPMDB (PLP mutants) 4.1.1.20
 
References
 Son HF, Kim KJ (2018) Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum Biochem Biophys Res Commun 495 1815-1821.

 Peverelli MG, Soares da Costa TP, Kirby N, Perugini MA (2016) Dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis J Biol Chem 291 9785-95.

 Oliver MR, Crowther JM, Leeman MM, Kessans SA, North RA, Donovan KA, Griffin MD, Suzuki H, Hudson AO, Kasanmascheff M, Dobson RC (2014) The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana Acta Crystallogr F Struct Biol Commun. 70 663-8.

 Tsujimoto N, Gunji Y, Ogawa-Miyata Y, Shimaoka M, Yasueda H. (2006) L-Lysine biosynthetic pathway of Methylophilus methylotrophus and construction of an L-lysine producer J Biotechnol 124 327-37.

 Hudson AO, Bless C, Macedo P, Chatterjee SP, Singh BK, Gilvarg C, Leustek T. (2005) Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways Biochim Biophys Acta 1721 27-36.

 Gokulan, K.; Rupp, B.; Pavelka, M.S. Jr,; Jacobs, W.R. Jr; Sacchettini, J.C. (2003) Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis J Biol Chem 278 18588-96.

 Ray, S.S.; Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley S.K. (2002) Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor Structure (Camb) 10 1499-508.

 Scapin, G.; Blanchard, J.S. (1998) Enzymology of bacterial lysine biosynthesis Adv Enzymol Relat Areas Mol Biol 72 279-324.

 Mills, D. A.; Flickinger, M. C. (1993) Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes Appl Environ Microbiol 59 2927-37.

 Martin, C.; Cami, B.; Borne, F.; Jeenes, D.J.; Haas, D.; Patte, J.C. (1986) Heterologous expression and regulation of the lysA genes of Pseudomonas aeruginosa and Escherichia coli Mol Gen Genet 203 430-4.

Articles on 4.1.1.20
 
last changed 2019/05/29 09:37

B6db activities