GenomeNet

Database: UniProt
Entry: Q04HB7
LinkDB: Q04HB7
Original site: Q04HB7 
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   16-JAN-2019, entry version 87.
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; Leuconostocaceae;
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.,
RA   Koonin E.V., Pavlov A., Pavlova N., Karamychev V., Polouchine N.,
RA   Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K.,
RA   Goodstein D.M., Hawkins T., Plengvidhya V., Welker D., Hughes J.,
RA   Goh Y., Benson A., Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B.,
RA   Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E.,
RA   Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C.,
RA   Breidt F., Broadbent J.R., Hutkins R., O'Sullivan D., Steele J.,
RA   Unlu G., Saier M.H. Jr., Klaenhammer T., Richardson P., Kozyavkin S.,
RA   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,
RP   AND 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:
RT   structural basis of substrate specificity.";
RL   J. Biochem. 152:505-508(2012).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
RP   PHOSPHATE, 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
RT   pyridoxal 5'-phosphate.";
RL   Acta Crystallogr. F 69:15-19(2013).
CC   -!- FUNCTION: Catalyzes the interconversion of D-lysine and L-lysine.
CC       Can 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,
CC         ChEBI:CHEBI:32551, 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,
CC         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
CC         D-lysine. kcat is 1.1 min(-1) for L-ornithine. kcat is 1.1 min(-
CC         1) for 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}.
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   ProteinModelPortal; Q04HB7; -.
DR   SMR; Q04HB7; -.
DR   STRING; 203123.OEOE_0162; -.
DR   PRIDE; Q04HB7; -.
DR   DNASU; 4416729; -.
DR   EnsemblBacteria; ABJ56155; ABJ56155; OEOE_0162.
DR   GeneID; 4416729; -.
DR   KEGG; ooe:OEOE_0162; -.
DR   eggNOG; ENOG4105CJ4; Bacteria.
DR   eggNOG; COG0787; LUCA.
DR   HOGENOM; HOG000031444; -.
DR   KO; K20707; -.
DR   OMA; SGAAMYH; -.
DR   OrthoDB; 859043at2; -.
DR   BioCyc; OOEN203123:OEOE_RS00765-MONOMER; -.
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; Complete proteome; Isomerase; Pyridoxal phosphate;
KW   Reference proteome.
FT   CHAIN         1    371       Lysine racemase.
FT                                /FTId=PRO_0000422274.
FT   ACT_SITE     39     39       Proton acceptor. {ECO:0000250}.
FT   ACT_SITE    266    266       Proton acceptor. {ECO:0000250}.
FT   BINDING     135    135       Substrate. {ECO:0000250}.
FT   BINDING     313    313       Substrate; via amide nitrogen.
FT                                {ECO:0000250}.
FT   MOD_RES      39     39       N6-(pyridoxal phosphate)lysine.
FT   MUTAGEN      39     39       K->A: Lack of activity. Does not bind
FT                                pyridoxal phosphate.
FT                                {ECO:0000269|PubMed:23035128}.
FT   MUTAGEN     224    224       T->I: Decreases activity. Shows weak
FT                                activity towards alanine.
FT                                {ECO:0000269|PubMed:23035128}.
FT   MUTAGEN     266    266       Y->A: Lack of activity.
FT                                {ECO:0000269|PubMed:23035128}.
FT   MUTAGEN     355    355       W->Y: Decreases activity. Shows weak
FT                                activity towards alanine.
FT                                {ECO:0000269|PubMed:23035128}.
FT   STRAND       10     14       {ECO:0000244|PDB:3CO8}.
FT   HELIX        15     29       {ECO:0000244|PDB:3CO8}.
FT   STRAND       32     37       {ECO:0000244|PDB:3CO8}.
FT   HELIX        39     43       {ECO:0000244|PDB:3CO8}.
FT   HELIX        47     54       {ECO:0000244|PDB:3CO8}.
FT   HELIX        55     57       {ECO:0000244|PDB:3CO8}.
FT   STRAND       61     66       {ECO:0000244|PDB:3CO8}.
FT   HELIX        67     75       {ECO:0000244|PDB:3CO8}.
FT   STRAND       82     84       {ECO:0000244|PDB:3CO8}.
FT   HELIX        90     92       {ECO:0000244|PDB:3CO8}.
FT   HELIX        93     98       {ECO:0000244|PDB:3CO8}.
FT   STRAND      102    105       {ECO:0000244|PDB:3CO8}.
FT   HELIX       108    117       {ECO:0000244|PDB:3CO8}.
FT   STRAND      123    129       {ECO:0000244|PDB:3CO8}.
FT   STRAND      131    133       {ECO:0000244|PDB:3CO8}.
FT   STRAND      135    138       {ECO:0000244|PDB:3CO8}.
FT   HELIX       141    153       {ECO:0000244|PDB:3CO8}.
FT   TURN        155    157       {ECO:0000244|PDB:3CO8}.
FT   STRAND      158    164       {ECO:0000244|PDB:3CO8}.
FT   HELIX       179    189       {ECO:0000244|PDB:3CO8}.
FT   STRAND      196    199       {ECO:0000244|PDB:3CO8}.
FT   HELIX       203    208       {ECO:0000244|PDB:3CO8}.
FT   HELIX       210    212       {ECO:0000244|PDB:3CO8}.
FT   STRAND      218    223       {ECO:0000244|PDB:3CO8}.
FT   TURN        224    228       {ECO:0000244|PDB:3CO8}.
FT   TURN        231    234       {ECO:0000244|PDB:3CO8}.
FT   STRAND      235    237       {ECO:0000244|PDB:3CO8}.
FT   HELIX       239    241       {ECO:0000244|PDB:3CO8}.
FT   STRAND      246    251       {ECO:0000244|PDB:3CO8}.
FT   STRAND      253    258       {ECO:0000244|PDB:3CO8}.
FT   STRAND      263    265       {ECO:0000244|PDB:3CO8}.
FT   HELIX       266    268       {ECO:0000244|PDB:3CO8}.
FT   STRAND      273    282       {ECO:0000244|PDB:3CO8}.
FT   HELIX       285    287       {ECO:0000244|PDB:3CO8}.
FT   HELIX       291    293       {ECO:0000244|PDB:3CO8}.
FT   STRAND      297    300       {ECO:0000244|PDB:3CO8}.
FT   STRAND      303    309       {ECO:0000244|PDB:3CO8}.
FT   STRAND      316    322       {ECO:0000244|PDB:3CO8}.
FT   STRAND      329    336       {ECO:0000244|PDB:3CO8}.
FT   STRAND      339    341       {ECO:0000244|PDB:3CO8}.
FT   HELIX       343    350       {ECO:0000244|PDB:3CO8}.
FT   HELIX       354    359       {ECO:0000244|PDB:3CO8}.
FT   STRAND      365    370       {ECO:0000244|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
//
DBGET integrated database retrieval system