ID A0JY83_ARTS2 Unreviewed; 500 AA.
AC A0JY83;
DT 12-DEC-2006, integrated into UniProtKB/TrEMBL.
DT 12-DEC-2006, sequence version 1.
DT 27-MAR-2024, entry version 108.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120};
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};
GN Name=lysA {ECO:0000256|HAMAP-Rule:MF_02120};
GN OrderedLocusNames=Arth_2624 {ECO:0000313|EMBL:ABK04003.1};
OS Arthrobacter sp. (strain FB24).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Micrococcaceae;
OC Arthrobacter.
OX NCBI_TaxID=290399 {ECO:0000313|EMBL:ABK04003.1, ECO:0000313|Proteomes:UP000000754};
RN [1] {ECO:0000313|Proteomes:UP000000754}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FB24 {ECO:0000313|Proteomes:UP000000754};
RX PubMed=24501649; DOI=10.4056/sigs.4438185;
RA Nakatsu C.H., Barabote R., Thompson S., Bruce D., Detter C., Brettin T.,
RA Han C., Beasley F., Chen W., Konopka A., Xie G.;
RT "Complete genome sequence of Arthrobacter sp. strain FB24.";
RL Stand. Genomic Sci. 9:106-116(2013).
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 -!- 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 -!- 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}.
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; CP000454; ABK04003.1; -; Genomic_DNA.
DR RefSeq; WP_011692465.1; NC_008541.1.
DR AlphaFoldDB; A0JY83; -.
DR STRING; 290399.Arth_2624; -.
DR KEGG; art:Arth_2624; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_11; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000754; 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 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 Lyase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000313|EMBL:ABK04003.1};
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};
KW Reference proteome {ECO:0000313|Proteomes:UP000000754}.
FT DOMAIN 88..339
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 380..455
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 427
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 291
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 333..336
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 396
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 400
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 428
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 457
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 457
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 101
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 500 AA; 52633 MW; 6FC085A7CB11D5D2 CRC64;
MSAQPGNSLN QASPLAPEWL DVPADLNALH EPMWAAGVAR NDAGELAIDG IPVSELQHEF
GTPLFVMSEN DFRARARAFS DAFNDAFADI CGGVDVYYAG KSFLCTAVVR WVEEEGLRLD
TASGGELAVA ARAGIPGADV ALHGNNKSDA EIHRALDMKL GRIVVDSLAE LERIAAIASA
RGETARVMLR LTPGVHAHTH EFIATAHEDQ KFGLSMAEDS TDQAGLSAAE EAVAAATGFA
GIELLGLHCH IGSQIFEPDG FALAAVKLLR FLAAMQEKYS IVLPELDLGG GYGIAYTPVD
TPRPPAEIAQ AMAAVVRSTC EELGITAPRI SIEPGRAIVG TSTFTLYEVG TLKTVRVDAP
AAADGAAADQ AGNTAKNVTY PRRYVSVDGG MSDNARPVLY DADYSAIVAS RTSGAAPQLS
RVVGKHCESG DIVVRDVYLP EDVAAGDLLA VPGTGAYCWA LSSNYNYLAR PGVVAVRDGS
ARLIVRGETE QDLLNRDMGV
//
