DOKDC_SALTY
ID DOKDC_SALTY Reviewed; 465 AA.
AC Q8ZNC4;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=D-ornithine/D-lysine decarboxylase {ECO:0000303|PubMed:29024617};
DE Short=D-Orn/D-Lys decarboxylase {ECO:0000303|PubMed:29024617};
DE Short=DOKDC {ECO:0000303|PubMed:29024617};
DE EC=4.1.1.116 {ECO:0000269|PubMed:29024617};
GN Name=dokD {ECO:0000303|PubMed:29024617};
GN OrderedLocusNames=STM2360 {ECO:0000312|EMBL:AAL21261.1};
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=LT2;
RX PubMed=29024617; DOI=10.1016/j.abb.2017.09.010;
RA Phillips R.S., Poteh P., Miller K.A., Hoover T.R.;
RT "STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella
RT enterica serovar typhimurium.";
RL Arch. Biochem. Biophys. 634:83-87(2017).
RN [3] {ECO:0007744|PDB:6N2H}
RP X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP REACTION MECHANISM, AND SUBUNIT.
RX PubMed=30699288; DOI=10.1021/acs.biochem.8b01319;
RA Phillips R.S., Poteh P., Krajcovic D., Miller K.A., Hoover T.R.;
RT "Crystal structure of D-ornithine/D-lysine decarboxylase, a stereoinverting
RT decarboxylase: implications for substrate specificity and stereospecificity
RT of fold III decarboxylases.";
RL Biochemistry 58:1038-1042(2019).
CC -!- FUNCTION: Catalyzes the decarboxylation of D-ornithine and D-lysine
CC (PubMed:29024617, PubMed:30699288). Ornithine is likely the
CC physiological substrate (PubMed:29024617). Has no detectable
CC diaminopimelate decarboxylase activity in vitro (PubMed:29024617).
CC {ECO:0000269|PubMed:29024617, ECO:0000269|PubMed:30699288}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ornithine + H(+) = CO2 + putrescine; Xref=Rhea:RHEA:59048,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57668,
CC ChEBI:CHEBI:326268; EC=4.1.1.116;
CC Evidence={ECO:0000269|PubMed:29024617, ECO:0000269|PubMed:30699288};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-lysine + H(+) = cadaverine + CO2; Xref=Rhea:RHEA:59052,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:32557,
CC ChEBI:CHEBI:58384; EC=4.1.1.116;
CC Evidence={ECO:0000269|PubMed:29024617, ECO:0000269|PubMed:30699288};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:29024617};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 1.8 sec(-1) with D-ornithine as substrate. kcat is 4.4
CC sec(-1) with D-lysine as substrate. {ECO:0000269|PubMed:29024617};
CC pH dependence:
CC Optimum pH is 6.5-8. {ECO:0000269|PubMed:29024617};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30699288}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000305}.
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DR EMBL; AE006468; AAL21261.1; -; Genomic_DNA.
DR RefSeq; NP_461302.1; NC_003197.2.
DR RefSeq; WP_000132305.1; NC_003197.2.
DR PDB; 6N2H; X-ray; 1.72 A; A=1-465.
DR PDBsum; 6N2H; -.
DR AlphaFoldDB; Q8ZNC4; -.
DR SMR; Q8ZNC4; -.
DR STRING; 99287.STM2360; -.
DR PaxDb; Q8ZNC4; -.
DR EnsemblBacteria; AAL21261; AAL21261; STM2360.
DR GeneID; 1253882; -.
DR KEGG; stm:STM2360; -.
DR PATRIC; fig|99287.12.peg.2498; -.
DR HOGENOM; CLU_026444_0_0_6; -.
DR OMA; YCRSMAS; -.
DR PhylomeDB; Q8ZNC4; -.
DR BioCyc; MetaCyc:STM2360-MON; -.
DR BioCyc; SENT99287:STM2360-MON; -.
DR BRENDA; 4.1.1.116; 5542.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR022643; De-COase2_C.
DR InterPro; IPR022644; De-COase2_N.
DR InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
DR Pfam; PF02784; Orn_Arg_deC_N; 1.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR PRINTS; PR01179; ODADCRBXLASE.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..465
FT /note="D-ornithine/D-lysine decarboxylase"
FT /id="PRO_0000451594"
FT ACT_SITE 387
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:B4XMC6"
FT BINDING 259
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:B4XMC6"
FT BINDING 307..310
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:B4XMC6"
FT BINDING 422
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:B4XMC6"
FT MOD_RES 80
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:B4XMC6"
FT HELIX 2..18
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 23..26
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 37..43
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 53..66
FT /evidence="ECO:0007829|PDB:6N2H"
FT TURN 67..69
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 85..93
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 103..112
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 119..121
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 140..144
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 147..160
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 164..170
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 197..205
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 210..216
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 227..247
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 252..255
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:6N2H"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 284..295
FT /evidence="ECO:0007829|PDB:6N2H"
FT TURN 296..298
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 300..306
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 310..313
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 317..332
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 338..348
FT /evidence="ECO:0007829|PDB:6N2H"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 356..359
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 369..371
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 378..383
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 385..388
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 401..404
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 413..418
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 430..432
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 437..441
FT /evidence="ECO:0007829|PDB:6N2H"
FT STRAND 447..451
FT /evidence="ECO:0007829|PDB:6N2H"
FT HELIX 456..460
FT /evidence="ECO:0007829|PDB:6N2H"
SQ SEQUENCE 465 AA; 52598 MW; A8716391D6AF707B CRC64;
MTDSIMQNYN QLREQVINGD RRFQHKDGHL CFEGVDLDAL ARQYPTPFYV FSEPEIIRNI
HEIQQAFAAH KNTKTFFASK TCSVMGVLKA IRDAGICAEA NSQYEVRKCL EIGFRGDQIV
FNGVVKKPAD LEYAIANDLY LINVDSLYEL EHIDAISRKL KKVANVCVRV EPNVPSATHA
ELVTAFHAKS GLDLEQAEET CRRILAMPYV HLRGLHMHVG DQVPESEPFA KATKVLVDES
RRLEEVLGIK FDLINVGGGI PVPYKYDDEN GDPLKDNMYA GITAQDFADA VIREVHKWRT
DVEICIEPGR KVTGSAAVLL TEVSCEKRKT NYDLNGNVEC HVEWKFVDAG YSVLSDSQHF
DWFFYVYNAS RMTAAHDAWI KLAGPLCDGG DYFHMGVKGE EFLLPKETHV GDIVAFLDAG
AYTIESQTVY NNRPRTGVVM IDKNGDTRLI RREDSYEDMV KYDIY
