LYSRA_THEMA
ID LYSRA_THEMA Reviewed; 354 AA.
AC Q9X1T3; G4FFY5;
DT 11-DEC-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Lysine racemase {ECO:0000303|PubMed:30548096};
DE Short=Lys racemase {ECO:0000303|PubMed:30548096};
DE EC=5.1.1.5 {ECO:0000269|PubMed:30548096};
DE AltName: Full=Ornithine racemase {ECO:0000305};
DE EC=5.1.1.12 {ECO:0000269|PubMed:30548096};
GN OrderedLocusNames=TM_1597 {ECO:0000312|EMBL:AAD36664.1};
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP PATHWAY, AND SUBUNIT.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=30548096; DOI=10.1111/febs.14720;
RA Miyamoto T., Katane M., Saitoh Y., Sekine M., Homma H.;
RT "Elucidation of the D-lysine biosynthetic pathway in the hyperthermophile
RT Thermotoga maritima.";
RL FEBS J. 286:601-614(2019).
CC -!- FUNCTION: Catalyzes the interconversion of D-lysine and L-lysine. Has
CC also high activity toward ornithine, and weaker activity toward
CC alanine. Contributes to production of D-lysine and D-alanine for use as
CC peptidoglycan components. {ECO:0000269|PubMed:30548096}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysine = D-lysine; Xref=Rhea:RHEA:22864, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:32557; EC=5.1.1.5;
CC Evidence={ECO:0000269|PubMed:30548096};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-ornithine = D-ornithine; Xref=Rhea:RHEA:11584,
CC ChEBI:CHEBI:46911, ChEBI:CHEBI:57668; EC=5.1.1.12;
CC Evidence={ECO:0000269|PubMed:30548096};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:30548096};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.14 mM for L-lysine {ECO:0000269|PubMed:30548096};
CC KM=1.77 mM for D-lysine {ECO:0000269|PubMed:30548096};
CC KM=1.13 mM for L-ornithine {ECO:0000269|PubMed:30548096};
CC KM=1.01 mM for D-ornithine {ECO:0000269|PubMed:30548096};
CC KM=375 mM for L-alanine {ECO:0000269|PubMed:30548096};
CC KM=282 mM for D-alanine {ECO:0000269|PubMed:30548096};
CC Vmax=16.9 umol/sec/mg enzyme with L-lysine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=16.3 umol/sec/mg enzyme with D-lysine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=13.1 umol/sec/mg enzyme with L-ornithine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=10.9 umol/sec/mg enzyme with D-ornithine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=23.5 umol/sec/mg enzyme with L-alanine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=17.7 umol/sec/mg enzyme with D-alanine as substrate
CC {ECO:0000269|PubMed:30548096};
CC Note=kcat is 693 sec(-1) with L-lysine as substrate. kcat is 669
CC sec(-1) with D-lysine as substrate. kcat is 537 sec(-1) with L-
CC ornithine as substrate. kcat is 447 sec(-1) with D-ornithine as
CC substrate. kcat is 965 sec(-1) with L-alanine as substrate. kcat is
CC 725 sec(-1) with D-alanine as substrate.
CC {ECO:0000269|PubMed:30548096};
CC pH dependence:
CC Optimum pH is 9.0-10.0. {ECO:0000269|PubMed:30548096};
CC Temperature dependence:
CC Optimum temperature is 85-95 degrees Celsius.
CC {ECO:0000269|PubMed:30548096};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000305|PubMed:30548096}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30548096}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. {ECO:0000305}.
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DR EMBL; AE000512; AAD36664.1; -; Genomic_DNA.
DR PIR; A72234; A72234.
DR RefSeq; NP_229397.1; NC_000853.1.
DR RefSeq; WP_004082040.1; NZ_CP011107.1.
DR AlphaFoldDB; Q9X1T3; -.
DR SMR; Q9X1T3; -.
DR STRING; 243274.THEMA_06265; -.
DR EnsemblBacteria; AAD36664; AAD36664; TM_1597.
DR KEGG; tma:TM1597; -.
DR KEGG; tmw:THMA_1637; -.
DR PATRIC; fig|243274.18.peg.1213; -.
DR InParanoid; Q9X1T3; -.
DR OMA; VGCFGGV; -.
DR OrthoDB; 859043at2; -.
DR BioCyc; MetaCyc:MON-21250; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008784; F:alanine racemase activity; IBA:GO_Central.
DR GO; GO:0018113; F:lysine racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0050157; F:ornithine racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.10; -; 1.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR029066; PLP-binding_barrel.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
PE 1: Evidence at protein level;
KW Cell shape; Cell wall biogenesis/degradation; Isomerase;
KW Peptidoglycan synthesis; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..354
FT /note="Lysine racemase"
FT /id="PRO_0000448682"
FT MOD_RES 36
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:P10724"
SQ SEQUENCE 354 AA; 39717 MW; FAF750F7823C42FE CRC64;
MVYPRLLINL KEIEENARKV VEMASRRGIE IVGVTKVTLG DPRFAETLRK AGIGILGESR
IRNVLRMKKA GIEGPFMLLR LPMMSELVED VKHFDYIMVS DPDVAKKVDE LSREMKRNVK
IIYMIDVGDL REGVWFEKAV EEIAQCRGAN IVGIGTNFGC YGGIIPTREK FEILLDIKEK
LEKNHGFNIE IVSGGNTPAL YALENGEIPE GINQLRIGEA IVLGRDITNN RVIDWLSQNT
FLIEAEVIEV KEKPSVPLGK RGLDVFGRKV DFVDRGIRKR AICALGEQDI DSRGLIPVDK
GVEVLHASSD HIVLDVTDFG DVKVGDVFRF RMTYSCLLKA MTSPFVEKVY EPSI
