ID R9SMY8_9EURY Unreviewed; 427 AA.
AC R9SMY8;
DT 18-SEP-2013, integrated into UniProtKB/TrEMBL.
DT 18-SEP-2013, sequence version 1.
DT 24-JAN-2024, entry version 49.
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 ECO:0000313|EMBL:AGN17524.1};
GN ORFNames=Abm4_1667 {ECO:0000313|EMBL:AGN17524.1};
OS Methanobrevibacter sp. AbM4.
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanobrevibacter.
OX NCBI_TaxID=224719 {ECO:0000313|EMBL:AGN17524.1, ECO:0000313|Proteomes:UP000014066};
RN [1] {ECO:0000313|EMBL:AGN17524.1, ECO:0000313|Proteomes:UP000014066}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AbM4 {ECO:0000313|EMBL:AGN17524.1};
RA Leahy S.C., Kelly W.J., Li D., Lambie S.C., Altermann E., Li Y.,
RA Attwood G.T.;
RL Submitted (JAN-2013) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AGN17524.1, ECO:0000313|Proteomes:UP000014066}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Abm4 {ECO:0000313|Proteomes:UP000014066};
RG Pastoral Greenhouse Gas Research Consortium;
RA Leahy S.C., Kelly W.J., Li D., Lambie S.C., Altermann E., Li Y.,
RA Attwood G.T.;
RT "The comlpete genome sequence of Methanobrevibacter sp. AbM4.";
RL Submitted (JUN-2013) 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; CP004050; AGN17524.1; -; Genomic_DNA.
DR RefSeq; WP_016359221.1; NC_021355.1.
DR AlphaFoldDB; R9SMY8; -.
DR STRING; 224719.Abm4_1667; -.
DR GeneID; 15799154; -.
DR KEGG; meb:Abm4_1667; -.
DR eggNOG; arCOG02268; Archaea.
DR HOGENOM; CLU_026444_0_2_2; -.
DR OrthoDB; 18565at2157; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000014066; 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; 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.
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:UP000014066}.
FT DOMAIN 44..289
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 290..378
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 351
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 240
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 282..285
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 285
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 320
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 324
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 352
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 380
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 380
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 64
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 427 AA; 47259 MW; D6313EBECF75E5BF CRC64;
MDLNIKVNDK DHLDIGGADA VDIANEFGTP VYAIDENRIR DNYNRFYNAF SKYYPDFKVF
YACKANTNLA VMKILESEGC CVDTVSPGEV YISEKLGFSP DRILFTGNNI TNEELKMVHD
MGVILNVDSR SALKRLAEVV DPKGLKVSIR VNPMVGAGHH EHTITGGVMS KFGIMDNEAT
EVYKLAQDLG FDPIGIHSHI GSGILDPEPF KLAIGSTMDI AGKVHEDLGI DFEFVDFGGG
IGVPYTPDEK ALDIDHFAHE NVEFFKGKLK EYNMKNPTMF LEPGRYIVAD AVTLLVQVNS
VKQSYRKYIG VDAGFNTLLR PCMYGSYHHI VDASKMSAPI TQEVDVAGDV CESGDLFARD
RPLPDIEEGD ILGILNSGAY GFTMASNYNS RPLPAEVLIK DGNPTLVRKA QTFDDLFRNQ
IIPDYLQ
//
