ID D7DXV4_NOSA0 Unreviewed; 463 AA.
AC D7DXV4;
DT 10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT 10-AUG-2010, sequence version 1.
DT 27-MAR-2024, entry version 80.
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 OrderedLocusNames=Aazo_4736 {ECO:0000313|EMBL:ADI65930.1};
OS Nostoc azollae (strain 0708) (Anabaena azollae (strain 0708)).
OC Bacteria; Cyanobacteriota; Cyanophyceae; Nostocales; Nostocaceae;
OC Trichormus.
OX NCBI_TaxID=551115 {ECO:0000313|EMBL:ADI65930.1, ECO:0000313|Proteomes:UP000001511};
RN [1] {ECO:0000313|EMBL:ADI65930.1, ECO:0000313|Proteomes:UP000001511}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=0708 {ECO:0000313|EMBL:ADI65930.1,
RC ECO:0000313|Proteomes:UP000001511};
RX PubMed=20628610; DOI=10.1371/journal.pone.0011486;
RA Ran L., Larsson J., Vigil-Stenman T., Nylander J.A., Ininbergs K.,
RA Zheng W.W., Lapidus A., Lowry S., Haselkorn R., Bergman B.;
RT "Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic
RT multicellular cyanobacterium.";
RL PLoS ONE 5:E11486-E11486(2010).
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; CP002059; ADI65930.1; -; Genomic_DNA.
DR RefSeq; WP_013192940.1; NC_014248.1.
DR AlphaFoldDB; D7DXV4; -.
DR STRING; 551115.Aazo_4736; -.
DR KEGG; naz:Aazo_4736; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_3; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000001511; 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; 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; 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:UP000001511}.
FT DOMAIN 77..323
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 324..414
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 387
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 274
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 316..319
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 319
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 356
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 360
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 388
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 416
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 416
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 97
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 463 AA; 50837 MW; E3B33E6129A1F109 CRC64;
MVSTHPLGIQ ASGSQYLPQK LNNTTLSPNQ ELLPLSARVN RHDSLEIGGC DVTTLVEQFG
SPLYILDEET LRTACRQYHD TFKQHYKDES QVLYASKAWN CLAVCAIVAS EGLGIDVVSG
GELYTALNAG VTPDKIYLHG NNKSRDELVL AIESGCTIVA DNWYELKTLV ELVTKSSPVR
IMLRLTPGIE CHTHEYIRTG HLDSKFGFDP SDLDEVFAFV SKQPSLNCVG LHAHIGSQIF
ERQPHRDLAA VMVQWLRDAA KYNLELKELN VGGGLGIKYT ESDDPPSIEE WSKAICEVVQ
QACAAENLPL PKLLCEPGRS LIATACVTAY SIGSAKVIPD LRTYVTIDGG MSDNPRPITY
QSVYRSVVAN KMSAALTETV TLAGKHCESG DILIKNAQLP KTEPGDILVV MGTGAYNYSM
ASNYNRLPRP AAVLVANGEA NLILQRENYQ DIIRQDCLPE RLK
//
