ID X4ZNH3_9BACL Unreviewed; 444 AA.
AC X4ZNH3;
DT 11-JUN-2014, integrated into UniProtKB/TrEMBL.
DT 11-JUN-2014, sequence version 1.
DT 24-JAN-2024, entry version 44.
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 ORFNames=PSAB_16190 {ECO:0000313|EMBL:AHV98145.1};
OS Paenibacillus sabinae T27.
OC Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
OX NCBI_TaxID=1268072 {ECO:0000313|EMBL:AHV98145.1, ECO:0000313|Proteomes:UP000019772};
RN [1] {ECO:0000313|EMBL:AHV98145.1, ECO:0000313|Proteomes:UP000019772}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=T27 {ECO:0000313|EMBL:AHV98145.1,
RC ECO:0000313|Proteomes:UP000019772};
RX PubMed=24651173;
RA Xie J.B., Du Z., Bai L., Tian C., Zhang Y., Xie J.Y., Wang T., Liu X.,
RA Chen X., Cheng Q., Chen S., Li J.;
RT "Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus
RT spp.: Organization, Evolution and Expression of the Nitrogen Fixation
RT Genes.";
RL PLoS Genet. 10:E1004231-E1004231(2014).
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; CP004078; AHV98145.1; -; Genomic_DNA.
DR RefSeq; WP_025335642.1; NZ_CP004078.1.
DR AlphaFoldDB; X4ZNH3; -.
DR STRING; 1268072.PSAB_16190; -.
DR KEGG; psab:PSAB_16190; -.
DR PATRIC; fig|1268072.3.peg.3346; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_9; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000019772; 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; 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.
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}.
FT DOMAIN 41..297
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 298..389
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 362
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 249
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 291..294
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 294
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 331
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 335
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="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 391
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 66
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 444 AA; 47877 MW; D745CF328B7B9751 CRC64;
MFLHGTSRIN DAGHLEIGGC DVTELKAEYG TPLYIVDEQL VRRRCREYMD AFAASGLGFQ
VAYASKAFSV MAMCRLADEE GLSLDVVSDG ELYTALQAGF PAERIHFHGN NKTPDEIEMA
LDARIGCFVV DNLVELELLQ AIAAEKNQTV NVLLRVTPGV EAHAHHAYAA TGQTDSKFGF
DIGNGSAQEA VRLASSKANL KLLGVHSHIG SQIFETEGFQ LAVERVAGFA RKVKEELGIE
FSVVNLGGGF GIRYVEGDTP LQVSEYVAAI TDAVKTHFAG IGSKLPEIWV EPGRSIVGDA
GTTLYTIGTS KEIPGVRKYV AVDGGMTDNP RPALYESKYE AVLANRAGEQ PEETVSIAGK
CCESGDMLIW DVELPKAESG DLLAVACTGA YNYSMASNYN RIRRPAVVFV QNGQSDLVVK
RESHGDIIAN DIVPARIAKQ PVTK
//
