BSR_PSEPK
ID BSR_PSEPK Reviewed; 409 AA.
AC Q88GJ9;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Broad specificity amino-acid racemase {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000305|PubMed:30008699};
DE EC=5.1.1.10 {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000269|PubMed:23995642};
DE AltName: Full=Broad spectrum racemase {ECO:0000303|PubMed:30008699};
DE Flags: Precursor;
GN Name=alr {ECO:0000303|PubMed:23995642, ECO:0000312|EMBL:AAN69319.1};
GN OrderedLocusNames=PP_3722 {ECO:0000312|EMBL:AAN69319.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=23995642; DOI=10.1128/jb.00761-13;
RA Radkov A.D., Moe L.A.;
RT "Amino acid racemization in Pseudomonas putida KT2440.";
RL J. Bacteriol. 195:5016-5024(2013).
RN [3]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=30008699; DOI=10.3389/fmicb.2018.01343;
RA Radkov A.D., Moe L.A.;
RT "A Broad Spectrum Racemase in Pseudomonas putida KT2440 Plays a Key Role in
RT Amino Acid Catabolism.";
RL Front. Microbiol. 9:1343-1343(2018).
CC -!- FUNCTION: Amino-acid racemase able to utilize a broad range of
CC substrates. Reversibly racemizes 9 of the 19 natural chiral amino acids
CC known, including both positively charged amino acids (Lys, Arg and His)
CC and non-beta-branched aliphatic amino acids (Ala, Leu, Met, Ser, Gln
CC and Asn). Among these amino acids, activity is the highest with lysine
CC and arginine, and poor or very poor with the others (PubMed:23995642).
CC Plays a primary role in the catabolism of basic amino acid, that allows
CC P.putida strain KT2440 to grow on L-Lys and L-Arg as the sole source of
CC carbon and nitrogen, through conversion to their respective D-
CC enantiomers (PubMed:30008699). {ECO:0000269|PubMed:23995642,
CC ECO:0000269|PubMed:30008699}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an L-alpha-amino acid = a D-alpha-amino acid;
CC Xref=Rhea:RHEA:18317, ChEBI:CHEBI:59869, ChEBI:CHEBI:59871;
CC EC=5.1.1.10; Evidence={ECO:0000255|HAMAP-Rule:MF_02212,
CC ECO:0000269|PubMed:23995642};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysine = D-lysine; Xref=Rhea:RHEA:22864, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:32557; Evidence={ECO:0000255|HAMAP-Rule:MF_02212,
CC ECO:0000269|PubMed:23995642, ECO:0000305|PubMed:30008699};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:22865;
CC Evidence={ECO:0000305|PubMed:30008699};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-arginine = D-arginine; Xref=Rhea:RHEA:18069,
CC ChEBI:CHEBI:32682, ChEBI:CHEBI:32689; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02212, ECO:0000269|PubMed:23995642,
CC ECO:0000305|PubMed:30008699};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18070;
CC Evidence={ECO:0000305|PubMed:30008699};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-glutamine = D-glutamine; Xref=Rhea:RHEA:59276,
CC ChEBI:CHEBI:58000, ChEBI:CHEBI:58359;
CC Evidence={ECO:0000269|PubMed:23995642};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02212};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.36 mM for D-lysine {ECO:0000269|PubMed:23995642};
CC KM=8.96 mM for L-lysine {ECO:0000269|PubMed:23995642};
CC KM=15.71 mM for D-alanine {ECO:0000269|PubMed:23995642};
CC KM=12.62 mM for L-alanine {ECO:0000269|PubMed:23995642};
CC Note=kcat is 274.5 sec(-1) with D-lysine as substrate. kcat is 1681.7
CC sec(-1) with L-lysine as substrate. kcat is 8.83 sec(-1) with D-
CC alanine as substrate. kcat is 7.33 sec(-1) with L-alanine as
CC substrate. Thus, the catalytic efficiency with lysine is nearly 3
CC orders of magnitude greater than that with alanine in both reaction
CC directions. {ECO:0000269|PubMed:23995642};
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000255|HAMAP-Rule:MF_02212,
CC ECO:0000269|PubMed:30008699}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene exhibit a limited
CC capacity for catabolism of L-Lys and L-Arg as the sole source of carbon
CC and nitrogen. They don't secrete D-Lys in the growth medium. The
CC stationary phase peptidoglycan structure does not differ between wild-
CC type and the deletion mutant strains, indicating that products
CC resulting from this enzyme activity are not incorporated into
CC peptidoglycan under these conditions. {ECO:0000269|PubMed:30008699}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. Bsr subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000305}.
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DR EMBL; AE015451; AAN69319.1; -; Genomic_DNA.
DR RefSeq; NP_745855.1; NC_002947.4.
DR RefSeq; WP_010954558.1; NC_002947.4.
DR AlphaFoldDB; Q88GJ9; -.
DR SMR; Q88GJ9; -.
DR STRING; 160488.PP_3722; -.
DR EnsemblBacteria; AAN69319; AAN69319; PP_3722.
DR KEGG; ppu:PP_3722; -.
DR PATRIC; fig|160488.4.peg.3967; -.
DR eggNOG; COG0787; Bacteria.
DR HOGENOM; CLU_028393_1_1_6; -.
DR OMA; TSMNTVM; -.
DR PhylomeDB; Q88GJ9; -.
DR BioCyc; MetaCyc:G1G01-3975-MON; -.
DR BioCyc; PPUT160488:G1G01-3975-MON; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0008784; F:alanine racemase activity; IEA:InterPro.
DR GO; GO:0047679; F:arginine racemase activity; IEA:RHEA.
DR GO; GO:0018113; F:lysine racemase activity; IEA:RHEA.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR CDD; cd06826; PLPDE_III_AR2; 1.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR HAMAP; MF_02212; Bsr_racemase; 1.
DR InterPro; IPR000821; Ala_racemase.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR011079; Ala_racemase_C.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR020622; Ala_racemase_pyridoxalP-BS.
DR InterPro; IPR029066; PLP-binding_barrel.
DR InterPro; IPR043698; Racemase_Bsr/Lyr.
DR Pfam; PF00842; Ala_racemase_C; 1.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR PRINTS; PR00992; ALARACEMASE.
DR SMART; SM01005; Ala_racemase_C; 1.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR00492; alr; 1.
DR PROSITE; PS00395; ALANINE_RACEMASE; 1.
PE 1: Evidence at protein level;
KW Disulfide bond; Isomerase; Periplasm; Pyridoxal phosphate;
KW Reference proteome; Signal.
FT SIGNAL 1..24
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT CHAIN 25..409
FT /note="Broad specificity amino-acid racemase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT /id="PRO_5004301730"
FT ACT_SITE 75
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT ACT_SITE 301
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT BINDING 174
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT MOD_RES 75
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT DISULFID 71..97
FT /evidence="ECO:0000250|UniProtKB:I0J1I6, ECO:0000255|HAMAP-
FT Rule:MF_02212"
SQ SEQUENCE 409 AA; 44224 MW; 90921393FDBFF5E7 CRC64;
MPFRRTLLAA SLALLITGQA PLYAAPPLSM DNGTNTLTVQ NSNAWVEVSA SALQHNIRTL
QAELAGKSKL CAVLKADAYG HGIGLVMPSI IAQGVPCVAV ASNEEARVVR ASGFTGQLVR
VRLASLSELE DGLQYDMEEL VGSAEFARQA DAIAARHGKT LRIHMALNSS GMSRNGVEMA
TWSGRGEALQ ITDQKHLKLV ALMTHFAVED KDDVRKGLAA FNEQTDWLIK HARLDRSKLT
LHAANSFATL EVPEARLDMV RTGGALFGDT VPARTEYKRA MQFKSHVAAV HSYPAGNTVG
YDRTFTLARD SRLANITVGY SDGYRRVFTN KGHVLINGHR VPVVGKVSMN TLMVDVTDFP
DVKGGNEVVL FGKQAGGEIT QAEMEEINGA LLADLYTVWG NSNPKILVD
