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B6db families: 4.1.1.17.1

4.1.1.17 1
Activity 4.1.1.17
Description Ornithine decarboxylase. (family 1)
Notes This compact family is formed by enzymes that belong to the fold type III group.
They are mostly of eukaryotic origin, although the family also includes two validated sequences from bacteria, and even a viral enzyme. (Actually, the Selenomonas and Vibrio enzymes are annotated as a Lys/Orn decarboxylases, since they decarboxylate with similar efficiency both L-lysine and L-ornithine).
In mammals, ornithine decarboxylase catalyzes the rate-limiting step of the pathway leading to the production of polyamines, which play an essential role in cell proliferation.
PDB 1D7K;2PLK;2NVA;
PLP Fold Type III
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type III

Number of sequences
45
Sequences in seed alignment
BacteriaNP_762948 (Vibrio vulnificus CMCP6); DCLO_SELRU (Selenomonas ruminantium); CAD78655 (Pirellula sp); NP_048554 (Paramecium bursaria Chlorella virus 1); ZP_01666158 (Thermosinus carboxydivorans Nor1);
FungiAAK38838 (Oculimacula yallundae); DCOR_YEAST (Saccharomyces cerevisiae); DCOR_SCHPO (Schizosaccharomyces pombe); DCOR_NEUCR (Neurospora crassa); EAA75548 (Gibberella zeae ); CAA61274 (Ustilago maydis); CAC80209 (Yarrowia lipolytica); DCOR_CANAL (Candida albicans); CAB61758 (Mucor circinelloides); AAF35284 (Coccidioides immitis); CAB56523 (Phaeosphaeria nodorum);
MetazoaEAA00421 (Anopheles gambiae ); DCOR_CAEEL (Caenorhabditis elegans); AAO92750 (Paralichthys olivaceus); DCOR_XENLA (Xenopus laevis); AAC27893 (Haemonchus contortus); DCOR_RAT (Rattus norvegicus); DCOR_BOVIN (Bos taurus); DCOR_MUSPA (Mus pahari); DCO1_DROME (Drosophila melanogaster); AAG01031 (Danio rerio); DCOR_MOUSE (Mus musculus); DCOR_CRIGR (Cricetulus griseus); DCOR_HUMAN (Homo sapiens); CAE71969 (Caenorhabditis briggsae); DCOR_PANRE (Panagrellus redivivus); AAA98981 (Musca domestica);
Other_EukaryaDCOR_LEIDO (Leishmania donovani); AAA30218 (Trypanosoma brucei); EAA41929 (Giardia lamblia ); AAD42894 (Leishmania tarentolae); CAA69402 (Crithidia fasciculata);
ViridiplantaeAAL87201 (Capsicum annuum); BAC79204 (Oryza sativa); AEQ02350 (Erythroxylum coca); AAG45222 (Nicotiana glutinosa); CAE46410 (Chlamydomonas reinhardtii); DCOR_DATST (Datura stramonium); CAD91349 (Glycine max); CAE02644 (Lotus corniculatus );

DISPLAY: Fasta format, alignment, hmm, hmm_local


Reference sequence DCOR_MOUSE
Domain interval 44-280
Catalytic site 69 K
 
References
 Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA. (2004) Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases J Biol Chem 282 27115-25.

 Lee JH, Son MY, Yoon MY, Choi JD, Kim YT. (2004) Isolation and characterization of ornithine decarboxylase gene from flounder (Paralichthys olivaceus) Mar Biotechnol (NY) 6 453-62.

 Shah R, Coleman CS, Mir K, Baldwin J, Van Etten JL, Grishin NV, Pegg AE, Stanley BA, Phillips MA. (2004) Paramecium bursaria chlorella virus-1 encodes an unusual arginine decarboxylase that is a close homolog of eukaryotic ornithine decarboxylases J Biol Chem 279 35760-7.

 Lee, Y.S.; Cho, Y.D. (2001) Identification of essential active-site residues in ornithine decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and L-lysine Biochem J 360 657-65.

 Almrud, J. J.; Oliveira, M. A.; Kern, A. D.; Grishin, N. V.; Phillips, M. A.; Hackert, M. L. (2000) Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding J Mol Biol 295 7-16..

 Guevara-Olvera, L.; Hung, C.Y.; Yu, J.J.; Cole, G.T. (2000) Sequence, expression and functional analysis of the Coccidioides immitis ODC (ornithine decarboxylase) gene Gene 25 437-48.

 Takatsuka, Y.; Yamaguchi, Y.; Ono, M.; Kamio, Y. (2000) Gene cloning and molecular characterization of lysine decarboxylase from Selenomonas ruminantium delineate its evolutionary relationship to ornithine decarboxylases from eukaryotes J Bacteriol 182 6732-41.

 Klein, R. D.; Favreau, M. A.; Alexander-Bowman, S. J.; Nulf, S. C.; Vanover, L.; Winterrowd, C. A.; Yarlett, N.; Martinez, M.; Keithly, J. S.; Zantello, M. R.; Thomas, E. M.; Geary, T. G. (1997) Haemonchus contortus: cloning and functional expression of a cDNA encoding ornithine decarboxylase and development of a screen for inhibitors Exp Parasitol 87 171-84.

 Michael, A.J.; Furze, J.M.; Rhodes M.J.; Burtin D. (1996) Molecular cloning and functional identification of a plant ornithine decarboxylase cDNA Biochem J 314 241-8.

 Niemann, G.; von Besser, H.; Walter, R. D. (1996) Panagrellus redivivus ornithine decarboxylase: structure of the gene, expression in Escherichia coli and characterization of the recombinant protein Biochem J 317 135-40.

 Fonzi, W. A. (1989) Biochemical and genetic characterization of the structure of yeast ornithine decarboxylase Biochem Biophys Res Commun 162 1409-16.

 Brabant, M.; McConlogue, L.; van Daalen Wetters, T.; Coffino, P. (1988) Mouse ornithine decarboxylase gene: cloning, structure, and expression Proc Natl Acad Sci U S A 85 2200-4.

 Phillips, M. A.; Coffino, P.; Wang, C. C. (1987) Cloning and sequencing of the ornithine decarboxylase gene from Trypanosoma brucei. Implications for enzyme turnover and selective difluoromethylornithine inhibition J Biol Chem 262 8721-7.

Articles on 4.1.1.17.1
last changed 2009/06/30 14:24

B6db families