LYSR_OENOB
ID LYSR_OENOB Reviewed; 371 AA.
AC Q04HB7;
DT 01-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 14-NOV-2006, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Lysine racemase;
DE EC=5.1.1.5;
GN OrderedLocusNames=OEOE_0162;
OS Oenococcus oeni (strain ATCC BAA-331 / PSU-1).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
OC Oenococcus.
OX NCBI_TaxID=203123;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-331 / PSU-1;
RX PubMed=17030793; DOI=10.1073/pnas.0607117103;
RA Makarova K.S., Slesarev A., Wolf Y.I., Sorokin A., Mirkin B., Koonin E.V.,
RA Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V.,
RA Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M.,
RA Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A.,
RA Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B., Smeianov V., Wechter W.,
RA Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y.,
RA Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J.R., Hutkins R.,
RA O'Sullivan D., Steele J., Unlu G., Saier M.H. Jr., Klaenhammer T.,
RA Richardson P., Kozyavkin S., Weimer B.C., Mills D.A.;
RT "Comparative genomics of the lactic acid bacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF LYS-39; THR-224; TYR-266 AND TRP-355.
RX PubMed=23035128; DOI=10.1093/jb/mvs120;
RA Kato S., Hemmi H., Yoshimura T.;
RT "Lysine racemase from a lactic acid bacterium, Oenococcus oeni: structural
RT basis of substrate specificity.";
RL J. Biochem. 152:505-508(2012).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE,
RP SUBUNIT, COFACTOR, AND PYRIDOXAL PHOSPHATE AT LYS-39.
RX PubMed=23295479; DOI=10.1107/s1744309112047276;
RA Palani K., Burley S.K., Swaminathan S.;
RT "Structure of alanine racemase from Oenococcus oeni with bound pyridoxal
RT 5'-phosphate.";
RL Acta Crystallogr. F 69:15-19(2013).
CC -!- FUNCTION: Catalyzes the interconversion of D-lysine and L-lysine. Can
CC also use arginine and ornithine, but not alanine.
CC {ECO:0000269|PubMed:23035128}.
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:23035128};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:23035128, ECO:0000269|PubMed:23295479};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=11 mM for L-lysine {ECO:0000269|PubMed:23035128};
CC KM=9.8 mM for D-lysine {ECO:0000269|PubMed:23035128};
CC KM=27 mM for L-ornithine {ECO:0000269|PubMed:23035128};
CC KM=22 mM for D-ornithine {ECO:0000269|PubMed:23035128};
CC Note=kcat is 2.1 min(-1) for L-lysine. kcat is 1.7 min(-1) for D-
CC lysine. kcat is 1.1 min(-1) for L-ornithine. kcat is 1.1 min(-1) for
CC D-ornithine.;
CC pH dependence:
CC Optimum pH is 9.0. {ECO:0000269|PubMed:23035128};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23295479}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. {ECO:0000305}.
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DR EMBL; CP000411; ABJ56155.1; -; Genomic_DNA.
DR RefSeq; WP_002818076.1; NC_008528.1.
DR PDB; 3CO8; X-ray; 1.70 A; A/B=3-371.
DR PDBsum; 3CO8; -.
DR AlphaFoldDB; Q04HB7; -.
DR SMR; Q04HB7; -.
DR STRING; 203123.OEOE_0162; -.
DR DNASU; 4416729; -.
DR EnsemblBacteria; ABJ56155; ABJ56155; OEOE_0162.
DR KEGG; ooe:OEOE_0162; -.
DR eggNOG; COG0787; Bacteria.
DR HOGENOM; CLU_028393_2_1_9; -.
DR OMA; ELMAVQH; -.
DR OrthoDB; 859043at2; -.
DR BRENDA; 5.1.1.5; 3009.
DR EvolutionaryTrace; Q04HB7; -.
DR Proteomes; UP000000774; Chromosome.
DR GO; GO:0008784; F:alanine racemase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0018113; F:lysine racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006522; P:alanine metabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR HAMAP; MF_01201; Ala_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 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; Isomerase; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..371
FT /note="Lysine racemase"
FT /id="PRO_0000422274"
FT ACT_SITE 39
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 266
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 39
FT /note="N6-(pyridoxal phosphate)lysine"
FT MUTAGEN 39
FT /note="K->A: Lack of activity. Does not bind pyridoxal
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23035128"
FT MUTAGEN 224
FT /note="T->I: Decreases activity. Shows weak activity
FT towards alanine."
FT /evidence="ECO:0000269|PubMed:23035128"
FT MUTAGEN 266
FT /note="Y->A: Lack of activity."
FT /evidence="ECO:0000269|PubMed:23035128"
FT MUTAGEN 355
FT /note="W->Y: Decreases activity. Shows weak activity
FT towards alanine."
FT /evidence="ECO:0000269|PubMed:23035128"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 15..29
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 39..43
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 47..54
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 61..66
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 93..98
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 108..117
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 141..153
FT /evidence="ECO:0007829|PDB:3CO8"
FT TURN 155..157
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 158..164
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 179..189
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 203..208
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:3CO8"
FT TURN 224..228
FT /evidence="ECO:0007829|PDB:3CO8"
FT TURN 231..234
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 263..265
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 273..282
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 285..287
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 291..293
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 303..309
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 316..322
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 329..336
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 343..350
FT /evidence="ECO:0007829|PDB:3CO8"
FT HELIX 354..359
FT /evidence="ECO:0007829|PDB:3CO8"
FT STRAND 365..370
FT /evidence="ECO:0007829|PDB:3CO8"
SQ SEQUENCE 371 AA; 41354 MW; 83A196C312B91E02 CRC64;
MVEAIHRSTR IEFSKSSLAY NVQYTKQVSG AKTLWLAVKS NAYGHGLLQV SKIARECGVD
GLAVSVLDEG IAIRQAGIDD FILILGPIDV KYAPIASKYH FLTTVSSLDW LKSADKILGK
EKLSVNLAVD TGMNRIGVRS KKDLKDEIEF LQEHSDHFSY DGIFTHFASS DNPDDHYFQR
QKNRWYELID GLIMPRYVHV MNSGAAMYHS KELPGCNSIA RVGTVVYGVE PSEGVLGPID
KLKPVFELKS ALTFVKKIPA GEGISYGSKF VTSRDTWIGT LPIGYGDGWL AEYQDFQLLI
DGQKCRQVGQ IAMDQMMVAL PHEYPIGTEV TLIGKSGKYE NTLYDLHKHS GVPPWKITVA
FSDRLKRMVV D
