ID A0A166IEM1_9MICO Unreviewed; 477 AA.
AC A0A166IEM1;
DT 06-JUL-2016, integrated into UniProtKB/TrEMBL.
DT 06-JUL-2016, sequence version 1.
DT 24-JAN-2024, entry version 28.
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:KZX22253.1};
GN ORFNames=ACH61_00581 {ECO:0000313|EMBL:KZX22253.1}, EV639_101255
GN {ECO:0000313|EMBL:TCO39310.1};
OS Rathayibacter tanaceti.
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae;
OC Rathayibacter.
OX NCBI_TaxID=1671680 {ECO:0000313|EMBL:KZX22253.1, ECO:0000313|Proteomes:UP000076717};
RN [1] {ECO:0000313|EMBL:TCO39310.1, ECO:0000313|Proteomes:UP000295366}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VKM Ac-2596 {ECO:0000313|EMBL:TCO39310.1,
RC ECO:0000313|Proteomes:UP000295366};
RX PubMed=26203337; DOI=.1186/s40793-015-0017-x;
RA Whitman W.B., Woyke T., Klenk H.P., Zhou Y., Lilburn T.G., Beck B.J.,
RA De Vos P., Vandamme P., Eisen J.A., Garrity G., Hugenholtz P.,
RA Kyrpides N.C.;
RT "Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III:
RT the genomes of soil and plant-associated and newly described type
RT strains.";
RL Stand. Genomic Sci. 10:26-26(2015).
RN [2] {ECO:0000313|EMBL:KZX22253.1, ECO:0000313|Proteomes:UP000076717}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VKM Ac-2596 {ECO:0000313|EMBL:KZX22253.1,
RC ECO:0000313|Proteomes:UP000076717};
RA Vasilenko O.V., Starodumova I.P., Tarlachkov S.V., Dorofeeva L.V.,
RA Evtushenko L.I.;
RT "Draft Genome Sequence of Rathayibacter sp. Strain VKM Ac-2596 Isolated
RT from Leaf Gall Induced by Plant-Parasitic Nematodes.";
RL Submitted (AUG-2015) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:TCO39310.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=VKM Ac-2596 {ECO:0000313|EMBL:TCO39310.1};
RA Whitman W., Huntemann M., Clum A., Pillay M., Palaniappan K., Varghese N.,
RA Mikhailova N., Stamatis D., Reddy T., Daum C., Shapiro N., Ivanova N.,
RA Kyrpides N., Woyke T.;
RL Submitted (MAR-2019) 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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KZX22253.1}.
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DR EMBL; LIIN01000011; KZX22253.1; -; Genomic_DNA.
DR EMBL; SLWP01000001; TCO39310.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A166IEM1; -.
DR PATRIC; fig|1671680.3.peg.615; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000076717; Unassembled WGS sequence.
DR Proteomes; UP000295366; Unassembled WGS sequence.
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|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:UP000076717}.
FT DOMAIN 91..325
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 326..425
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 397
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 277
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 319..322
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 366
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 370
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 398
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 427
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 427
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 99
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 477 AA; 50354 MW; B29E873C021FEDF3 CRC64;
MVIDAARAPQ HPLAPDWLRT PDDANELVEG IWSDGARRDA DGVLWVAGVA ATELVRRYGT
PLYVVDEADA RRRAVELRDV FARELARIGT GVTVYYAGKA FLSTEVARWM RGEGLNLDLS
SGGEMAVALA AGIEPERFGL HGNNKSLAEI DRAVEVGAGT IVLDSLLEIE RVAAAAERHG
RVQAVRLRVN SGVHAHTHEF LATAHEDQKF GLALADCPAA VARIRSFPSL RFLGLHCHIG
SQIFGAGGFA ESASRLLDVH AALLADGPVP ELNLGGGFGI AYTSADDPTP IAEIAAAVAD
AVAEQCAVRG IPVPHIAIEP GRSLIGPAGL TLYEVGTVKD VVVGPEGATA VRRYVSVDGG
MSDNARPALY GADYTALLAN RSSSAEPALV RVAGKHCESG DIVVHDDFLP ADVGPGDLLA
VAATGAYCWS LASNYNYLGR PPVVAVRDGR SRVLVHGETE EDLLRRDAGI ERKATSR
//
