ID D1BCT2_SANKS Unreviewed; 462 AA.
AC D1BCT2;
DT 19-JAN-2010, integrated into UniProtKB/TrEMBL.
DT 19-JAN-2010, sequence version 1.
DT 27-MAR-2024, entry version 83.
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=Sked_09810 {ECO:0000313|EMBL:ACZ20930.1};
OS Sanguibacter keddieii (strain ATCC 51767 / DSM 10542 / NCFB 3025 / ST-74).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Sanguibacteraceae;
OC Sanguibacter.
OX NCBI_TaxID=446469 {ECO:0000313|EMBL:ACZ20930.1, ECO:0000313|Proteomes:UP000000322};
RN [1] {ECO:0000313|EMBL:ACZ20930.1, ECO:0000313|Proteomes:UP000000322}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51767 / DSM 10542 / NCFB 3025 / ST-74
RC {ECO:0000313|Proteomes:UP000000322};
RX PubMed=21304646;
RA Ivanova N., Sikorski J., Sims D., Brettin T., Detter J.C., Han C.,
RA Lapidus A., Copeland A., Glavina Del Rio T., Nolan M., Chen F., Lucas S.,
RA Tice H., Cheng J.F., Bruce D., Goodwin L., Pitluck S., Pati A.,
RA Mavromatis K., Chen A., Palaniappan K., D'haeseleer P., Chain P.,
RA Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Goker M., Pukall R.,
RA Klenk H.P., Kyrpides N.C.;
RT "Complete genome sequence of Sanguibacter keddieii type strain (ST-74).";
RL Stand. Genomic Sci. 1:110-118(2009).
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; CP001819; ACZ20930.1; -; Genomic_DNA.
DR AlphaFoldDB; D1BCT2; -.
DR STRING; 446469.Sked_09810; -.
DR KEGG; ske:Sked_09810; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_11; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000322; 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; 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; 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|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW Rule:MF_02120};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120,
KW ECO:0000256|PIRSR:PIRSR600183-50}.
FT DOMAIN 71..321
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 326..418
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 390
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 273
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 315..318
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 318
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 359
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 363
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 391
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 420
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 420
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 87
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 462 AA; 48306 MW; FF950332E27E1702 CRC64;
MSGHPAAGAA AARPLEQHVW PTTAALTTDG ELTLAGLTAT DLARDFGTPA FVLDEQHFRD
RARLFRDSFS EAFGSVGAEV DVYYAGKSFL SVAVARWARE EGLRVDTCTG GELAVALRAG
VPGAEIGLHG NNKSDDEITR AIEAEVGRIV VDSFAEIDRV AELARAAGRD GGARVPVMVR
VTTGIHAGGH EFISTAHEDQ KFGVSLTGGQ ALAALQAVLE HPELELLGAH THIGSQIQDA
AAFEANARKM LALRAELQAA TGYLLPELDL GGGYGIAYVP SDVPIDVPAL ARDLADVVGS
VCAELGTTVP RISIEPGRSV VGSTTVTLYT VGVVKPVTLE DGSVRTYVSV DGGMSDNIRP
ALYEAEYTAR LANRTGSAET VAARVVGKHC ESGDIVISDI ELPADVARGD LLAVPATGAY
GRSMASNYNH VLRPPVVAVA DGAARVIVRR ETEDDLLSLD VG
//
