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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 phylogenesis.

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

PDB 1HKW;1TWI;5X7M;
PLP Fold Type III
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type III

Number of sequences 43
Sequences in seed alignment
ArchaeaCAF30756 (Methanococcus maripaludis); DCDA_METTH (Methanobacterium thermoautotrophicum); DCDA_ARCFU (Archaeoglobus fulgidus); NP_394250 (Thermoplasma acidophilum); BAB59962 (Thermoplasma volcanium); DCDA_METJA (Methanococcus jannaschii);
BacteriaDCDA_MYCSM (Mycobacterium smegmatis); DCDA_HAEIN (Haemophilus influenzae); DCDA_AQUAE (Aquifex aeolicus); ZP_00044746 (Magnetococcus sp. MC-1); AAR33493 (Geobacter sulfurreducens); DCDA_CORGL (Corynebacterium glutamicum); CAE30181 (Rhodopseudomonas palustris); AAG42251 (Staphylococcus aureus); BAC92756 (Methylophilus methylotrophus); AAP78104 (Helicobacter hepaticus); DCDA_BACSU (Bacillus subtilis); CAD85868 (Nitrosomonas europaea); DCDA_STRCO (Streptomyces coelicolor); DCDA_MYCTU (Mycobacterium tuberculosis); DCDA_ECOLI (Escherichia coli); DCDA_ZYMMO (Zymomonas mobilis); DCDA_BACHD (Bacillus halodurans); DCDA_CAMJE (Campylobacter jejuni); DCDA_VIBCH (Vibrio cholerae); DCDA_PSEAE (Pseudomonas aeruginosa); DCDA_ACTPA (Actinosynnema pretiosum (subsp. auranticum)); BAC68626 (Streptomyces avermitilis); DCDA_NEIMA (Neisseria meningitidis (serogroup A)); AAS96124 (Desulfovibrio vulgaris); CAE09483 (Wolinella succinogenes); CAE13485 (Photorhabdus luminescens); DCDA_HELPY (Helicobacter pylori); DCDA_BACMT (Bacillus methanolicus); ZP_00061104 (Clostridium thermocellum); NP_404421 (Yersinia pestis); DCDA_THEMA (Thermotoga maritima);
ViridiplantaeBAD16980 (Oryza sativa); CAO47588 (Vitis vinifera); EDQ70110 (Physcomitrella patens); XP_001690241 (Chlamydomonas reinhardtii); DCDA1_ARATH (Arabidopsis thaliana); DCDA2_ARATH (Arabidopsis thaliana);

DISPLAY: Fasta format, alignment, hmm, hmm_local


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

 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 2017/12/19 10:04

B6db families