B6db families : 4_1_1

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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

Sequences in seed alignment

Archaea	DCDA_METJA (Methanococcus jannaschii); DCDA_ARCFU (Archaeoglobus fulgidus); NP_394250 (Thermoplasma acidophilum); DCDA_METTH (Methanobacterium thermoautotrophicum); CAF30756 (Methanococcus maripaludis); BAB59962 (Thermoplasma volcanium);
Bacteria	DCDA_ACTPA (Actinosynnema pretiosum (subsp. auranticum)); DCDA_BACSU (Bacillus subtilis); DCDA_THEMA (Thermotoga maritima); CAE30181 (Rhodopseudomonas palustris); DCDA_CORGL (Corynebacterium glutamicum); DCDA_AQUAE (Aquifex aeolicus); DCDA_ECOLI (Escherichia coli); CAE09483 (Wolinella succinogenes); DCDA_MYCTU (Mycobacterium tuberculosis); AAR33493 (Geobacter sulfurreducens); NP_404421 (Yersinia pestis); BAC92756 (Methylophilus methylotrophus); DCDA_PSEAE (Pseudomonas aeruginosa); DCDA_MYCSM (Mycobacterium smegmatis); ZP_00044746 (Magnetococcus sp. MC-1); AAS96124 (Desulfovibrio vulgaris); DCDA_ZYMMO (Zymomonas mobilis); CAE13485 (Photorhabdus luminescens); DCDA_VIBCH (Vibrio cholerae); AAP78104 (Helicobacter hepaticus); CAD85868 (Nitrosomonas europaea); ZP_00061104 (Clostridium thermocellum); DCDA_STRCO (Streptomyces coelicolor); BAC68626 (Streptomyces avermitilis); DCDA_NEIMA (Neisseria meningitidis (serogroup A)); DCDA_BACHD (Bacillus halodurans); AAG42251 (Staphylococcus aureus); DCDA_HELPY (Helicobacter pylori); DCDA_CAMJE (Campylobacter jejuni); DCDA_HAEIN (Haemophilus influenzae); DCDA_BACMT (Bacillus methanolicus);
Viridiplantae	CAO47588 (Vitis vinifera); XP_001690241 (Chlamydomonas reinhardtii); EDQ70110 (Physcomitrella patens); DCDA1_ARATH (Arabidopsis thaliana); BAD16980 (Oryza sativa); DCDA2_ARATH (Arabidopsis thaliana);

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