ID F1YT12_9PROT Unreviewed; 447 AA.
AC F1YT12;
DT 31-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 31-MAY-2011, sequence version 1.
DT 24-JAN-2024, entry version 61.
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:EGE48036.1};
GN ORFNames=APO_1070 {ECO:0000313|EMBL:EGE48036.1};
OS Acetobacter pomorum DM001.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales;
OC Acetobacteraceae; Acetobacter.
OX NCBI_TaxID=945681 {ECO:0000313|EMBL:EGE48036.1, ECO:0000313|Proteomes:UP000018454};
RN [1] {ECO:0000313|EMBL:EGE48036.1, ECO:0000313|Proteomes:UP000018454}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DM001 {ECO:0000313|EMBL:EGE48036.1,
RC ECO:0000313|Proteomes:UP000018454};
RX PubMed=22053049; DOI=10.1126/science.1212782;
RA Shin S.C., Kim S.H., You H., Kim B., Kim A.C., Lee K.A., Yoon J.H.,
RA Ryu J.H., Lee W.J.;
RT "Drosophila microbiome modulates host developmental and metabolic
RT homeostasis via insulin signaling.";
RL Science 334:670-674(2011).
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:EGE48036.1}.
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DR EMBL; AEUP01000023; EGE48036.1; -; Genomic_DNA.
DR RefSeq; WP_006116124.1; NZ_AEUP01000023.1.
DR AlphaFoldDB; F1YT12; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000018454; 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; 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 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.
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|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:UP000018454}.
FT DOMAIN 58..300
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 301..395
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 368
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 262
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 296..299
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 299
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 340
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 369
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 397
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 397
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 83
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 447 AA; 47211 MW; E90748E80BFA5BF6 CRC64;
MAETPVYTDA DPTLAELLQT HPQLTVSPTC GLMLEGVALN AIADSVGTPC WVLGAGTLRT
RMRRMHAAMR DAGLDVSIHY AVKANDHLAI LTLIGQEGFG ADIVSGGELA RAIKAGIPAS
RIVFSGVGKT DAELEQAISH GIGQINVESA EELEAISAIA TKLGKQATIT LRINPDVDAK
THAKITTGLA ANKFGIPFQD AAALYAHAFT LSGVRPVGFA THIGSQILTT TPYRAAYARV
AELVRSVRAA GNAVSVVDCG GGLGICYRNE TEGQPEALAG AIKAELGDLG VKLAIEPGRW
PIGPAGVLLS SVILRKEQGM DVPFLVLDTA MNELLRPSMY DAWHGILPLA PQAFSQPVSL
AHVVGPVCES GDTFARDRLL PPLARNARIA LLDTGAYGAV MSSTYNSRPL AAEVLVEDGQ
WQVIRQRQSV EELWQDETVP SHLAKAT
//
