DCLO_SELRU
ID DCLO_SELRU Reviewed; 393 AA.
AC O50657; Q7DFY1;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Lysine/ornithine decarboxylase;
DE Short=LDC;
DE EC=4.1.1.17;
DE EC=4.1.1.18;
GN Name=ldc;
OS Selenomonas ruminantium.
OC Bacteria; Firmicutes; Negativicutes; Selenomonadales; Selenomonadaceae;
OC Selenomonas.
OX NCBI_TaxID=971;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-28; 30-37; 52-64;
RP 153-163; 276-288 AND 344-352, AND MUTAGENESIS OF 44-ALA--VAL-46; PRO-54;
RP GLY-319; SER-322; ILE-326 AND GLY-350.
RC STRAIN=Subsp. lactilytica;
RX PubMed=11073919; DOI=10.1128/jb.182.23.6732-6741.2000;
RA Takatsuka Y., Yamaguchi Y., Ono M., Kamio Y.;
RT "Gene cloning and molecular characterization of lysine decarboxylase from
RT Selenomonas ruminantium delineate its evolutionary relationship to
RT ornithine decarboxylases from eukaryotes.";
RL J. Bacteriol. 182:6732-6741(2000).
CC -!- FUNCTION: Decarboxylates both L-lysine and L-ornithine with similar
CC catalytic efficiency.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-lysine = cadaverine + CO2; Xref=Rhea:RHEA:22352,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:58384; EC=4.1.1.18;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-ornithine = CO2 + putrescine; Xref=Rhea:RHEA:22964,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:46911,
CC ChEBI:CHEBI:326268; EC=4.1.1.17;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- ACTIVITY REGULATION: Inhibited competitively by both alpha-
CC difluoromethyllysine and alpha-difluoromethylornithine.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.5 mM for L-lysine;
CC KM=0.96 mM for L-ornithine;
CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via
CC L-ornithine pathway; putrescine from L-ornithine: step 1/1.
CC -!- SUBUNIT: Homodimer.
CC -!- MISCELLANEOUS: Mutagen studies showed that it is possible to convert
CC S.ruminantium LDC to an enzyme with a preference for decarboxylating L-
CC ornithine when five amino acid residues (Ala-44, Gly-45, Val-46, Pro-54
CC and Ser-322) were replaced with the corresponding ones found in mouse
CC ODC.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000305}.
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DR EMBL; AB011029; BAA24923.1; -; Genomic_DNA.
DR EMBL; AB104737; BAC57940.1; -; Genomic_DNA.
DR PDB; 5GJM; X-ray; 2.91 A; A/B=1-393.
DR PDB; 5GJN; X-ray; 2.00 A; A=1-393.
DR PDB; 5GJO; X-ray; 1.80 A; A/B=1-393.
DR PDB; 5GJP; X-ray; 2.50 A; A=1-393.
DR PDBsum; 5GJM; -.
DR PDBsum; 5GJN; -.
DR PDBsum; 5GJO; -.
DR PDBsum; 5GJP; -.
DR AlphaFoldDB; O50657; -.
DR SMR; O50657; -.
DR OMA; SFFVCDL; -.
DR BioCyc; MetaCyc:MON-12423; -.
DR BRENDA; 4.1.1.18; 5668.
DR BRENDA; 4.1.1.B12; 5668.
DR SABIO-RK; O50657; -.
DR UniPathway; UPA00535; UER00288.
DR GO; GO:0008923; F:lysine decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0004586; F:ornithine decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0033387; P:putrescine biosynthetic process from ornithine; IEA:UniProtKB-UniPathway.
DR GO; GO:0008295; P:spermidine biosynthetic process; IEA:UniProtKB-KW.
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; 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; IPR002433; Orn_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
DR PANTHER; PTHR11482; PTHR11482; 1.
DR Pfam; PF02784; Orn_Arg_deC_N; 1.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR PRINTS; PR01179; ODADCRBXLASE.
DR PRINTS; PR01182; ORNDCRBXLASE.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Direct protein sequencing; Lyase;
KW Polyamine biosynthesis; Putrescine biosynthesis; Pyridoxal phosphate;
KW Spermidine biosynthesis.
FT CHAIN 1..393
FT /note="Lysine/ornithine decarboxylase"
FT /id="PRO_0000149910"
FT ACT_SITE 323
FT /note="Proton donor; shared with dimeric partner"
FT /evidence="ECO:0000250"
FT MOD_RES 51
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT MUTAGEN 44..46
FT /note="AGV->VTP: 2-fold increase in substrate specificity
FT towards ornithine. 5-fold increase in substrate specificity
FT towards ornithine; when associated with D-54. 70-fold
FT increase in substrate specificity towards ornithine; when
FT associated with D-54 and A-322. 16-fold increase in
FT substrate specificity towards ornithine; when associated
FT with D-54; T-322 and L-326."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 52
FT /note="A->C: No change in substrate specificity."
FT MUTAGEN 54
FT /note="P->D: 3-fold increase in substrate specificity
FT towards ornithine. 5-fold increase in substrate specificity
FT towards ornithine; when associated with 44-V--P-46. 70-fold
FT increase in substrate specificity towards ornithine; when
FT associated with 44-V--P-46 and A-322. 16-fold increase in
FT substrate specificity towards ornithine; when associated
FT with 44-V--P-46; T-322 and L-326."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 319
FT /note="G->W: 7-fold increase in substrate specificity
FT towards ornithine."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 322
FT /note="S->A: 29-fold increase in substrate specificity
FT towards ornithine. 70-fold increase in substrate
FT specificity towards ornithine; when associated with 44-V--
FT P-46 and D-54."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 322
FT /note="S->T: 16-fold increase in substrate specificity
FT towards ornithine; when associated with L-326. 16-fold
FT increase in substrate specificity towards ornithine; when
FT associated with 44-V--P-46; D-54 and L-326."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 326
FT /note="I->L: 16-fold increase in substrate specificity
FT towards ornithine; when associated with T-322. 16-fold
FT increase in substrate specificity towards ornithine; when
FT associated with 44-V--P-46; D-54 and T-322."
FT /evidence="ECO:0000269|PubMed:11073919"
FT MUTAGEN 350
FT /note="G->D: Loss of dimer formation and decarboxylase
FT activity."
FT /evidence="ECO:0000269|PubMed:11073919"
FT HELIX 8..17
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 20..25
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 27..40
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 56..64
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 74..82
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 99..108
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 121..127
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:5GJP"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 142..146
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 156..158
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 159..168
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 188..206
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 232..246
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 258..262
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 265..275
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 277..280
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 282..287
FT /evidence="ECO:0007829|PDB:5GJO"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 295..298
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 305..307
FT /evidence="ECO:0007829|PDB:5GJM"
FT STRAND 314..319
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 328..335
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 343..346
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 360..362
FT /evidence="ECO:0007829|PDB:5GJO"
FT STRAND 368..370
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 371..373
FT /evidence="ECO:0007829|PDB:5GJO"
FT HELIX 375..383
FT /evidence="ECO:0007829|PDB:5GJO"
SQ SEQUENCE 393 AA; 43214 MW; 66249907E2061167 CRC64;
MKNFRLSEKE VKTLAKRIPT PFLVASLDKV EENYQFMRRH LPRAGVFYAM KANPTPEILS
LLAGLGSHFD VASAGEMEIL HELGVDGSQM IYANPVKDAR GLKAAADYNV RRFTFDDPSE
IDKMAKAVPG ADVLVRIAVR NNKALVDLNT KFGAPVEEAL DLLKAAQDAG LHAMGICFHV
GSQSLSTAAY EEALLVARRL FDEAEEMGMH LTDLDIGGGF PVPDAKGLNV DLAAMMEAIN
KQIDRLFPDT AVWTEPGRYM CGTAVNLVTS VIGTKTRGEQ PWYILDEGIY GCFSGIMYDH
WTYPLHCFGK GNKKPSTFGG PSCDGIDVLY RDFMAPELKI GDKVLVTEMG SYTSVSATRF
NGFYLAPTII FEDQPEYAAR LTEDDDVKKK AAV
