ID A0A1Z5H7B6_9GAMM Unreviewed; 414 AA.
AC A0A1Z5H7B6;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 24-JAN-2024, entry version 23.
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=bplSymb_SCF00402P031 {ECO:0000313|EMBL:GAW85190.1};
OS Bathymodiolus platifrons methanotrophic gill symbiont.
OC Bacteria; Pseudomonadota; Gammaproteobacteria.
OX NCBI_TaxID=113268 {ECO:0000313|EMBL:GAW85190.1, ECO:0000313|Proteomes:UP000196430};
RN [1] {ECO:0000313|EMBL:GAW85190.1, ECO:0000313|Proteomes:UP000196430}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HPD1508-B01-01 {ECO:0000313|EMBL:GAW85190.1,
RC ECO:0000313|Proteomes:UP000196430};
RX PubMed=28453654; DOI=10.1093/gbe/evx082;
RA Takishita K., Takaki Y., Chikaraishi Y., Ikuta T., Ozawa G., Yoshida T.,
RA Ohkouchi N., Fujikura K.;
RT "Genomic Evidence that Methanotrophic Endosymbionts Likely Provide Deep-Sea
RT Bathymodiolus Mussels with a Sterol Intermediate in Cholesterol
RT Biosynthesis.";
RL Genome Biol. Evol. 9:1148-1160(2017).
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:GAW85190.1}.
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DR EMBL; BDMN01000033; GAW85190.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Z5H7B6; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000196430; 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:UP000196430}.
FT DOMAIN 35..279
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 280..369
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 343
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 239
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 273..276
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 276
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 312
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 316
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 344
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 371
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 371
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 60
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 414 AA; 45558 MW; 2C75A2E3C4400A65 CRC64;
MDYFNYRENS LCAEDVAIEE IVTEYGSPCY IYSKATLERH WHAFDSAFGK QAHLICYAVK
ANSNIAILNT LARLGSGFDI VSLGELERVL VAKGDPKKVV FSGVGKREDE IRAALQAGIR
CFNIEVKGEL DRINQIAGEL GMIAPVSFRV NPDVDAKTHP YISTGLKENK FGIDIAGALG
EYRRAAAMQH IEIVGIDCHI GSQLTETRPF LDALDRVLKI VDALKAEGIN LHHLDLGGGL
GICYNDETPP EPAEYVAALL ERLGHNELEI LLEPGRAIAG NAGILVTKVE YLKPTEHKNF
AIVDAAMNDL VRPSLYSSWQ AIIPVQLGSK ELEKVWDIVG PVCETGDFLG KDRCLALREG
DLLAIRSSGA YGFTMSSNYN SRPRVAELMV DGENTHLIRE RETIAQLWAG EHLL
//
