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B6db families: 4.1.1.20

4.1.1.20
Activity 4.1.1.20
Description Diaminopimelate decarboxylase.
Notes Compact family, including archaeal, bacterial and plant enzymes. The gene genealogies do not seem to correlate with organismal philogenesis.

In plants, diaminopimelate decarboxylase activity appears to reside entirely within chloroplasts.

PDB 1HKW;1TWI;
PLP Fold Type III
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type III

Number of sequences
43
Sequences in seed alignment
ArchaeaNP_394250 (Thermoplasma acidophilum); DCDA_ARCFU (Archaeoglobus fulgidus); DCDA_METTH (Methanobacterium thermoautotrophicum); BAB59962 (Thermoplasma volcanium); DCDA_METJA (Methanococcus jannaschii); CAF30756 (Methanococcus maripaludis);
BacteriaNP_404421 (Yersinia pestis); DCDA_BACHD (Bacillus halodurans); DCDA_ECOLI (Escherichia coli); AAS96124 (Desulfovibrio vulgaris); CAE13485 (Photorhabdus luminescens); DCDA_ACTPA (Actinosynnema pretiosum (subsp. auranticum)); AAR33493 (Geobacter sulfurreducens); CAD85868 (Nitrosomonas europaea); DCDA_VIBCH (Vibrio cholerae); DCDA_CAMJE (Campylobacter jejuni); DCDA_PSEAE (Pseudomonas aeruginosa); DCDA_HAEIN (Haemophilus influenzae); DCDA_HELPY (Helicobacter pylori); DCDA_ZYMMO (Zymomonas mobilis); DCDA_AQUAE (Aquifex aeolicus); DCDA_BACMT (Bacillus methanolicus); DCDA_MYCSM (Mycobacterium smegmatis); DCDA_THEMA (Thermotoga maritima); DCDA_CORGL (Corynebacterium glutamicum); AAP78104 (Helicobacter hepaticus); AAG42251 (Staphylococcus aureus); CAE09483 (Wolinella succinogenes); DCDA_BACSU (Bacillus subtilis); BAC68626 (Streptomyces avermitilis); ZP_00044746 (Magnetococcus sp. MC-1); DCDA_STRCO (Streptomyces coelicolor); DCDA_NEIMA (Neisseria meningitidis (serogroup A)); CAE30181 (Rhodopseudomonas palustris); DCDA_MYCTU (Mycobacterium tuberculosis); ZP_00061104 (Clostridium thermocellum); BAC92756 (Methylophilus methylotrophus);
ViridiplantaeEDQ70110 (Physcomitrella patens); BAD16980 (Oryza sativa); DCDA1_ARATH (Arabidopsis thaliana); DCDA2_ARATH (Arabidopsis thaliana); XP_001690241 (Chlamydomonas reinhardtii); CAO47588 (Vitis vinifera);

DISPLAY: Fasta format, alignment, hmm, hmm_local


Reference sequence DCDA_ECOLI
Domain interval 32-297
Catalytic site 54 K
 
References
 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.

 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 2008/09/12 15:17

B6db families