BSR_PSEPU
ID BSR_PSEPU Reviewed; 409 AA.
AC I6LNY0;
DT 01-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 1.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=Broad specificity amino-acid racemase {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000303|PubMed:23118975};
DE EC=5.1.1.10 {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000269|PubMed:23118975};
DE Flags: Precursor;
GN Name=bar {ECO:0000303|PubMed:23118975};
GN Synonyms=alr {ECO:0000312|EMBL:ADW54426.1};
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=YZ-26;
RX PubMed=22806802; DOI=10.1007/s11274-011-0816-1;
RA Liu J.L., Liu X.Q., Shi Y.W.;
RT "Expression, purification, and characterization of alanine racemase from
RT Pseudomonas putida YZ-26.";
RL World J. Microbiol. Biotechnol. 28:267-274(2012).
RN [2] {ECO:0007744|PDB:4DYJ, ECO:0007744|PDB:4FS9}
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEX WITH PLP, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITES,
RP REACTION MECHANISM, SUBUNIT, MUTAGENESIS OF ARG-174; ASN-175 AND ALA-393,
RP AND DISULFIDE BOND.
RC STRAIN=DSM 84 / IMG 1513;
RX PubMed=23118975; DOI=10.1371/journal.pone.0048301;
RA Wu H.M., Kuan Y.C., Chu C.H., Hsu W.H., Wang W.C.;
RT "Crystal structures of lysine-preferred racemases, the non-antibiotic
RT selectable markers for transgenic plants.";
RL PLoS ONE 7:E48301-E48301(2012).
CC -!- FUNCTION: Amino-acid racemase that catalyzes the interconversion of L-
CC lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975).
CC To a lesser extent, is also able to interconvert alanine and isoleucine
CC enantiomers (PubMed:23118975, PubMed:22806802).
CC {ECO:0000269|PubMed:22806802, ECO:0000269|PubMed:23118975}.
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:23118975};
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:23118975};
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:23118975};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-alanine = D-alanine; Xref=Rhea:RHEA:20249,
CC ChEBI:CHEBI:57416, ChEBI:CHEBI:57972;
CC Evidence={ECO:0000269|PubMed:22806802, ECO:0000269|PubMed:23118975};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02212,
CC ECO:0000269|PubMed:22806802, ECO:0000269|PubMed:23118975};
CC -!- ACTIVITY REGULATION: Activity is enhanced by Co(2+), Mn(2+) and Sr(2+),
CC and decreased by Cu(2+). {ECO:0000269|PubMed:22806802}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=10.34 mM for L-alanine {ECO:0000269|PubMed:22806802};
CC KM=25.4 mM for L-lysine {ECO:0000269|PubMed:23118975};
CC KM=14.5 mM for L-arginine {ECO:0000269|PubMed:23118975};
CC Vmax=18.73 mmol/min/mg enzyme with L-alanine as substrate
CC {ECO:0000269|PubMed:22806802};
CC Note=kcat is 4238 min(-1) with L-alanine as substrate
CC (PubMed:22806802). kcat is 3545 min(-1) with L-lysine as substrate.
CC kcat is 2228 min(-1) with L-arginine as substrate (PubMed:23118975).
CC {ECO:0000269|PubMed:22806802, ECO:0000269|PubMed:23118975};
CC pH dependence:
CC Optimum pH is 9.0. {ECO:0000269|PubMed:22806802};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:22806802};
CC -!- SUBUNIT: Monomer (PubMed:22806802). Forms a head-to-tail homodimer in
CC the structure (PubMed:23118975). {ECO:0000269|PubMed:22806802,
CC ECO:0000269|PubMed:23118975}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000250|UniProtKB:Q88GJ9,
CC ECO:0000255|HAMAP-Rule:MF_02212}.
CC -!- MISCELLANEOUS: The active-site cleft is located at the dimeric
CC interface and contains the two conserved catalytic residues, a lysine
CC from one subunit and a tyrosine from the other subunit.
CC {ECO:0000305|PubMed:23118975}.
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; GU462155; ADW54426.1; -; Genomic_DNA.
DR PDB; 4DYJ; X-ray; 2.45 A; A/B=1-409.
DR PDB; 4FS9; X-ray; 3.10 A; A/B=1-409.
DR PDBsum; 4DYJ; -.
DR PDBsum; 4FS9; -.
DR AlphaFoldDB; I6LNY0; -.
DR SMR; I6LNY0; -.
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 3D-structure; Disulfide bond; Isomerase; Periplasm; Pyridoxal phosphate;
KW 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_0000422273"
FT ACT_SITE 75
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000305|PubMed:23118975"
FT ACT_SITE 301
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000305|PubMed:23118975"
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 ECO:0000269|PubMed:23118975"
FT DISULFID 71..97
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000269|PubMed:23118975"
FT MUTAGEN 174
FT /note="R->A,K: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23118975"
FT MUTAGEN 175
FT /note="N->L: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23118975"
FT MUTAGEN 393
FT /note="A->Y: Reduces the catalytic activity towards L-Lys
FT by 2-fold. Loss of racemase activity towards L-Arg."
FT /evidence="ECO:0000269|PubMed:23118975"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:4FS9"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 50..64
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 67..73
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 83..92
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 103..111
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 116..122
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 126..131
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 138..141
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 144..156
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 161..167
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 174..177
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 182..192
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 197..203
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 211..231
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 240..242
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 246..251
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 258..263
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 281..293
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:4FS9"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 308..317
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:4DYJ"
FT TURN 329..331
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 333..336
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 339..343
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 352..355
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 367..374
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 381..388
FT /evidence="ECO:0007829|PDB:4DYJ"
FT HELIX 393..402
FT /evidence="ECO:0007829|PDB:4DYJ"
FT STRAND 405..408
FT /evidence="ECO:0007829|PDB:4DYJ"
SQ SEQUENCE 409 AA; 44217 MW; 03D668FBAD9C87E7 CRC64;
MPFRRTLLAA SLVLLITGQA PLYAAPPLSM DNGTNALTVQ NSNAWVEVSA SALQHNIRTL
QAELAGKSRL CAVLKADAYG HGIGLVMPSI IAQGVPCVAV ASNEEARVVR ASGFTGQLVR
VRAASLSELE DALQYDMEEL VGSAEFARQA DAIAARHGKT LRIHLAFNSS GMSRNGVEMA
TWSGRGEALQ ITDQKHLELV ALMTHFAVED KDDVRKGLAA FNEQTDWLIK HARLDRSKLT
LHAANSFATL EVPEARLDMV RTGGALFGDT VPGRTEYKRA MQFKSRVAAV HSYPAGNTVG
YDRTFTLARD SRLANITVGY SDGYRRVFTN KGHVLINGHR VPVVGKVSMN TLMVDVTDFP
DVKGGNEVVL FGKQAGGEIT QAEMEEINGA LLADLYTVWG SSNPKILVD
