ID R9GX17_9SPHI Unreviewed; 386 AA.
AC R9GX17;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 24-JAN-2024, entry version 44.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|RuleBase:RU003738};
DE EC=4.1.1.20 {ECO:0000256|RuleBase:RU003738};
GN ORFNames=ADIARSV_0699 {ECO:0000313|EMBL:EOR96055.1};
OS Arcticibacter svalbardensis MN12-7.
OC Bacteria; Bacteroidota; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Arcticibacter.
OX NCBI_TaxID=1150600 {ECO:0000313|EMBL:EOR96055.1, ECO:0000313|Proteomes:UP000014174};
RN [1] {ECO:0000313|EMBL:EOR96055.1, ECO:0000313|Proteomes:UP000014174}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MN12-7 {ECO:0000313|EMBL:EOR96055.1,
RC ECO:0000313|Proteomes:UP000014174};
RX PubMed=23846277;
RA Shivaji S., Ara S., Prasad S., Manasa B.P., Begum Z., Singh A.,
RA Kumar Pinnaka A.;
RT "Draft Genome Sequence of Arcticibacter svalbardensis Strain MN12-7T, a
RT Member of the Family Sphingobacteriaceae Isolated from an Arctic Soil
RT Sample.";
RL Genome Announc. 1:E00484-13(2013).
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|RuleBase:RU003738};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|PIRSR:PIRSR600183-50, 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|RuleBase:RU003738}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000256|RuleBase:RU003737}.
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:EOR96055.1}.
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DR EMBL; AQPN01000024; EOR96055.1; -; Genomic_DNA.
DR RefSeq; WP_016193945.1; NZ_AQPN01000024.1.
DR AlphaFoldDB; R9GX17; -.
DR STRING; 1150600.ADIARSV_0699; -.
DR PATRIC; fig|1150600.3.peg.686; -.
DR eggNOG; COG0019; Bacteria.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000014174; Unassembled WGS sequence.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR CDD; cd06828; PLPDE_III_DapDC; 1.
DR Gene3D; 3.20.20.10; Alanine racemase; 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|RuleBase:RU003738};
KW Decarboxylase {ECO:0000256|RuleBase:RU003738};
KW Lyase {ECO:0000256|RuleBase:RU003738, ECO:0000313|EMBL:EOR96055.1};
KW Lysine biosynthesis {ECO:0000256|RuleBase:RU003738};
KW Pyridoxal phosphate {ECO:0000256|PIRSR:PIRSR600183-50};
KW Reference proteome {ECO:0000313|Proteomes:UP000014174}.
FT DOMAIN 17..364
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 30..272
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT ACT_SITE 337
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT MOD_RES 48
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 386 AA; 43740 MW; F716DCDCFE251CB5 CRC64;
MFSKETLAGF NTRKTPFYYY DLKLLKETLS ACKDAANEYG FQVHYAMKAN FNERVLKCIQ
GFGFGADCVS GNEVKKAVEV GFPSNQVVFA GVGKSDDEII TALELNIYCF NVESVQELEI
INDLAAGVGK RARVALRINP NVDAYTHHNI TTGLEENKFG INQWELPACA EYLNRAQNIW
LEGIHFHIGS QITNLTVFKS LCVRVNEIKL WFEERGFNLK ILNVGGGLGV DYYHPDENKI
ADFKAYFEIF NQFLDRKPGQ EVHFELGRAL VAHCGTLISR VLYVKNGIKK HFLVLDAGMT
ELMRPALYQA YHKMENLSRN VELEQSIMKY DIVGPICEST DCFGKEVEIG TSFRGDLIAI
RTAGAYGDVM SSRYNLREQL EPYYTE
//
