1. MARTIN, C., CAMI, B., YEH, P., STRAGIER, P., PARSOT, C. AND PATTE, J.-C.
Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary
relationship with other amino acid decarboxylases.
MOL.BIOL.EVOL. 5 549-559 (1988).
2. SANDMEIER, E., HALE, T.I. AND CHRISTEN, P.
Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid
EUR.J.BIOCHEMISTRY 221 997-1002 (1994).
3. MILLS, D.A. AND FLICKINGER, M.C.
Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene
from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes.
APPL.ENVIRON.MICROBIOL. 59 2927-2937( 1993).
4. POULIN, R., LU, L., ACKERMANN, B., BEY, P. AND PEGG, A.E.
Mechanism of the irreversible inactivation of mouse ornithine decarboxylase
by alpha-difluoromethylornithine. Characterization of sequences at the
inhibitor and coenzyme binding sites.
J.BIOL.CHEM. 267 150-158 (1992).
Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-,
arginine- and related substrates can be classified into different families
on the basis of sequence similarity [1,2]. One of these families includes:
eukaryotic ornithine decarboxylase (ODC), which catalyses the transformation
of ornithine into putrescine; prokaryotic diaminopimelic acid decarboxylase
(DAPDC), which catalyses the conversion of diaminopimelic acid into lysine,
the final step of lysine biosynthesis; Pseudomonas syringae pv. tabaci
protein, tabA, which is probably involved in tabtoxin biosynthesis and
is similar to DAPDC; and bacterial and plant biosynthetic arginine
decarboxylase (ADC), which catalyses the transformation of arginine
into agmatine, the first step in putrescine synthesis from arginine.
Although these proteins, which are known collectively as group IV
decarboxylases , probably share a common evolutionary origin, their
levels of sequence similarity are low, being confined to a few short
conserved regions. These conserved motifs suggest a common structural
arrangement for positioning of substrate and the cofactor pyridoxal
5'-phosphate among bacterial DAP decarboxylases, eukaryotic ornithine
decarboxylases and arginine decarboxylases .
DAPDCRBXLASE is a 4-element fingerprint that provides a signature for
diaminopimelate decarboxylases. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those sections
that characterise the diaminopimelate decarboxylases but distinguish them
from the rest of the ODA family. Four iterations on SPTR37_10f were required
to reach convergence, at which point a true set comprising 19 sequences was
identified. A single partial match was found, TABA_PSESZ, Pseudomonas
syringae tabA protein, which matches motifs 3 and 4.