ID F0S1S9_DESTD Unreviewed; 420 AA.
AC F0S1S9;
DT 03-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 03-MAY-2011, sequence version 1.
DT 27-MAR-2024, entry version 69.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
DE Short=DAP decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120};
DE Short=DAPDC {ECO:0000256|HAMAP-Rule:MF_02120};
DE EC=4.1.1.20 {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
GN Name=lysA {ECO:0000256|HAMAP-Rule:MF_02120};
GN OrderedLocusNames=Dester_0277 {ECO:0000313|EMBL:ADY72934.1};
OS Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA).
OC Bacteria; Aquificota; Aquificae; Desulfurobacteriales;
OC Desulfurobacteriaceae; Desulfurobacterium.
OX NCBI_TaxID=868864 {ECO:0000313|EMBL:ADY72934.1, ECO:0000313|Proteomes:UP000007102};
RN [1] {ECO:0000313|EMBL:ADY72934.1, ECO:0000313|Proteomes:UP000007102}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11699 / BSA {ECO:0000313|Proteomes:UP000007102};
RX PubMed=22675590; DOI=10.4056/sigs.2465574;
RA Goker M., Daligault H., Mwirichia R., Lapidus A., Lucas S., Deshpande S.,
RA Pagani I., Tapia R., Cheng J.F., Goodwin L., Pitluck S., Liolios K.,
RA Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K.,
RA Han C., Land M., Hauser L., Pan C., Brambilla E.M., Rohde M., Spring S.,
RA Sikorski J., Wirth R., Detter J.C., Woyke T., Bristow J., Eisen J.A.,
RA Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of the thermophilic sulfur-reducer
RT Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea
RT hydrothermal vent.";
RL Stand. Genomic Sci. 5:407-415(2011).
RN [2] {ECO:0000313|Proteomes:UP000007102}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11699 / BSA {ECO:0000313|Proteomes:UP000007102};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Bruce D., Goodwin L., Pitluck S.,
RA Kyrpides N., Mavromatis K., Pagani I., Ivanova N., Mikhailova N.,
RA Daligault H., Detter J.C., Tapia R., Han C., Land M., Hauser L.,
RA Markowitz V., Cheng J.-F., Hugenholtz P., Woyke T., Wu D., Spring S.,
RA Brambilla E., Klenk H.-P., Eisen J.A.;
RT "The complete genome of Desulfurobacterium thermolithotrophum DSM 11699.";
RL Submitted (FEB-2011) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000256|HAMAP-
CC Rule:MF_02120}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine;
CC Xref=Rhea:RHEA:15101, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:57791; EC=4.1.1.20;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_02120,
CC ECO:0000256|RuleBase:RU003738};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|PIRSR:PIRSR600183-50,
CC ECO:0000256|RuleBase:RU003738};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_02120}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000256|HAMAP-Rule:MF_02120}.
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DR EMBL; CP002543; ADY72934.1; -; Genomic_DNA.
DR RefSeq; WP_013637893.1; NC_015185.1.
DR AlphaFoldDB; F0S1S9; -.
DR STRING; 868864.Dester_0277; -.
DR KEGG; dte:Dester_0277; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_0_0; -.
DR InParanoid; F0S1S9; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000007102; Chromosome.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
DR CDD; cd06828; PLPDE_III_DapDC; 1.
DR Gene3D; 3.20.20.10; Alanine racemase; 1.
DR HAMAP; MF_02120; LysA; 1.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR002986; DAP_deCOOHase_LysA.
DR InterPro; IPR022643; De-COase2_C.
DR InterPro; IPR022657; De-COase2_CS.
DR InterPro; IPR022644; De-COase2_N.
DR InterPro; IPR022653; De-COase2_pyr-phos_BS.
DR InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
DR NCBIfam; TIGR01048; lysA; 1.
DR PANTHER; PTHR43727; DIAMINOPIMELATE DECARBOXYLASE; 1.
DR PANTHER; PTHR43727:SF2; DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC-RELATED; 1.
DR Pfam; PF02784; Orn_Arg_deC_N; 1.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR PRINTS; PR01181; DAPDCRBXLASE.
DR PRINTS; PR01179; ODADCRBXLASE.
DR SUPFAM; SSF50621; Alanine racemase C-terminal domain-like; 1.
DR SUPFAM; SSF51419; PLP-binding barrel; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120};
KW Decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120,
KW ECO:0000256|RuleBase:RU003738};
KW Lyase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
KW Lysine biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120,
KW ECO:0000256|RuleBase:RU003738};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120,
KW ECO:0000256|PIRSR:PIRSR600183-50};
KW Reference proteome {ECO:0000313|Proteomes:UP000007102}.
FT DOMAIN 35..375
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 43..285
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT ACT_SITE 348
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 244
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 279..282
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 282
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 318
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 377
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 377
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 65
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 420 AA; 46397 MW; 427C6C382ADBEED2 CRC64;
MREELFPFIY YENGKLKIDG ISVEELARKY GTPLYVYSQS ALEHWFKEFD SAFSSIEHIT
CFAVKSNSNI SVLKVLKELG AGADTVSMGE IFRALTAGID PKKIVFAGVG KRIDEIEYGL
EKGILMFNVE SESELYAINR VAEKLGKVAP IAFRVNPDVN PKTHPYISTG LKTSKFGIAY
EGAIELYKKA KNLKNINPIG IHFHIGSQIT DVSVFGEAAR KIKEIVKELY SVGIEIEYFD
AGGGLGISYN PNEPPVPARA LADEIIPIIK DLGCKLILEP GRRLAGNAGI LLSQVIYKKE
RHEKLFYIVD AGMNDLARPS LYKAYHHIVP ASKKEGNLKK ADVVGPICET GDILAEDREL
PPLNEGDIIA VLSAGAYGFT MASNYNSRPR PAEVIAKEGR AEIIRQRETL GDLISKEEIF
//
