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B6db families: b
Description Lysine decarboxylase (family b)
Notes A compact family of proteins mostly from enterobacteria.
The sequences are related to those in family 4.1.17_2 (bacterial ornithine decarboxylases) and 4.1.19_2 (Arginine decarboxylases).
In addition to the PLP-dependent domain, they encompass two additional, smaller domains (one at the N-terminus, the other at the N-terminus).
The enzyme from Burkholderia sp. AIU 395 also shows a minor Lys oxidase activity.
PDB 3Q16;6Q6I;
PLP Fold Type I
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type I

Number of sequences
Sequences in seed alignment
BacteriaBAP47521 (Burkholderia sp. AIU 395); NP_250509 (Pseudomonas aeruginosa); WP_063647004 (Aliivibrio fischeri); DCLZ_ECOLI (Escherichia coli); WP_032824097 (Haemophilus influenzae); AAD18126 (Eikenella corrodens); AQU15094 (uncultured bacterium); DCLY_SALTY (Salmonella typhimurium); DCLY_HAFAL (Hafnia alvei); DCLY_ECOLI (Escherichia coli); NP_799269 (Vibrio parahaemolyticus); BAB16718 (Moritella japonica); WP_011079948 (Vibrio vulnificus); WP_024270753 (Shinella sp. DD12); SED96662 (Paraburkholderia caballeronis);

DISPLAY: Fasta format, alignment, hmm, hmm_local

Reference sequence DCLZ_ECOLI
Domain interval 130-562
Catalytic site 367 K
 Han L, Yuan J, Ao X, Lin S, Han X, Ye H (2018) Biochemical Characterization and Phylogenetic Analysis of the Virulence Factor Lysine Decarboxylase From Vibrio vulnificus Front Microbiol 9 3082.

 Deng J, Gao H, Gao Z, Zhao H, Yang Y, Wu Q, Wu B, Jiang C (2017) Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms PLoS One 12 e0185060.

 Kanjee U1, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA. (2011) Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. 30 931-44.

 Chou HT, Hegazy M, Lu CD (2010) L-lysine catabolism is controlled by L-arginine and ArgR in Pseudomonas aeruginosa PAO1 J Bacteriol 192 5874-80.

 Sugawara A, Matsui D, Takahashi N, Yamada M, Asano Y, Isobe K (2010) Characterization of a pyridoxal-5'-phosphate-dependent l-lysine decarboxylase/oxidase from Burkholderia sp. AIU 395 J Biosci Bioeng 118 496-501.

 Levine, M.; Progulske-Fox, A.; Denslow, N.D.; Farmerie, W.G.; Smith, D.M.; Swearingen, W.T.; Miller, F.C.; Liang, Z.; Roe, B.A.; Pan, H.Q. (2001) Identification of lysine decarboxylase as a mammalian cell growth inhibitor in Eikenella corrodens: possible role in periodontal disease Microb Pathog 30 179-92.

 Lemonnier, M.; Lane, D. (1998) Expression of the second lysine decarboxylase gene of Escherichia coli Microbiology 144 751-60.

 Yamamoto, S.; Imamura, T.; Kusaba, K.; Shinoda, S. (1991) Purification and some properties of inducible lysine decarboxylase from Vibrio parahaemolyticus Chem Pharm Bull (Tokyo) 39 3067-70..

 Fecker, L.F.; Beier, H.; Berlin, J. (1986) Cloning and characterization of a lysine decarboxylase gene from Hafnia alvei Mol Gen Genet 203 177-184.

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last changed 2019/12/12 18:41

B6db families