ID   KRDE_DESAH              Reviewed;         354 AA.
AC   C0QM06;
DT   09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT   05-MAY-2009, sequence version 1.
DT   03-AUG-2022, entry version 65.
DE   RecName: Full=L-Lys-D/L-Arg epimerase;
DE            EC=5.1.1.-;
DE   AltName: Full=Cationic dipeptide epimerase;
GN   OrderedLocusNames=HRM2_12000;
OS   Desulforapulum autotrophicum (strain ATCC 43914 / DSM 3382 / VKM B-1955 /
OS   HRM2) (Desulfobacterium autotrophicum).
OC   Bacteria; Proteobacteria; Deltaproteobacteria; Desulfobacterales;
OC   Desulfobacteraceae; Desulforapulum.
OX   NCBI_TaxID=177437;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43914 / DSM 3382 / VKM B-1955 / HRM2;
RX   PubMed=19187283; DOI=10.1111/j.1462-2920.2008.01825.x;
RA   Strittmatter A.W., Liesegang H., Rabus R., Decker I., Amann J., Andres S.,
RA   Henne A., Fricke W.F., Martinez-Arias R., Bartels D., Goesmann A.,
RA   Krause L., Puehler A., Klenk H.P., Richter M., Schuler M., Gloeckner F.O.,
RA   Meyerdierks A., Gottschalk G., Amann R.;
RT   "Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate
RT   reducer oxidizing organic carbon completely to carbon dioxide.";
RL   Environ. Microbiol. 11:1038-1055(2009).
RN   [2]
RP   FUNCTION, AND COFACTOR.
RX   PubMed=22392983; DOI=10.1073/pnas.1112081109;
RA   Lukk T., Sakai A., Kalyanaraman C., Brown S.D., Imker H.J., Song L.,
RA   Fedorov A.A., Fedorov E.V., Toro R., Hillerich B., Seidel R.,
RA   Patskovsky Y., Vetting M.W., Nair S.K., Babbitt P.C., Almo S.C.,
RA   Gerlt J.A., Jacobson M.P.;
RT   "Homology models guide discovery of diverse enzyme specificities among
RT   dipeptide epimerases in the enolase superfamily.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:4122-4127(2012).
CC   -!- FUNCTION: Catalyzes the epimerization of L-Lys-L-Arg to L-Lys-D-Arg (in
CC       vitro). Catalyzes the epimerization of positively charged dipeptides,
CC       with a preference for substrates with a basic amino acid in the second
CC       position. Has epimerase activity with L-Lys-L-Lys, L-Arg-L-Arg, L-Val-
CC       L-Arg, L-Val-L-Lys and L-Ala-L-Arg (in vitro).
CC       {ECO:0000269|PubMed:22392983}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:22392983};
CC       Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:22392983};
CC   -!- MISCELLANEOUS: Part of a large, functionally divergent protein family.
CC       Protein modeling and substrate docking was used to predict the
CC       substrate specificity, prior to biochemical analysis.
CC   -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC       enzyme family. {ECO:0000305}.
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DR   EMBL; CP001087; ACN14312.1; -; Genomic_DNA.
DR   RefSeq; WP_015903101.1; NC_012108.1.
DR   AlphaFoldDB; C0QM06; -.
DR   SMR; C0QM06; -.
DR   STRING; 177437.HRM2_12000; -.
DR   EnsemblBacteria; ACN14312; ACN14312; HRM2_12000.
DR   KEGG; dat:HRM2_12000; -.
DR   eggNOG; COG4948; Bacteria.
DR   HOGENOM; CLU_030273_4_0_7; -.
DR   OMA; HEEFPVT; -.
DR   OrthoDB; 951991at2; -.
DR   Proteomes; UP000000442; Chromosome.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0016854; F:racemase and epimerase activity; IDA:UniProtKB.
DR   GO; GO:0016855; F:racemase and epimerase activity, acting on amino acids and derivatives; IEA:InterPro.
DR   GO; GO:0006518; P:peptide metabolic process; IDA:UniProtKB.
DR   CDD; cd03319; L-Ala-DL-Glu_epimerase; 1.
DR   Gene3D; 3.20.20.120; -; 1.
DR   Gene3D; 3.30.390.10; -; 1.
DR   InterPro; IPR034603; Dipeptide_epimerase.
DR   InterPro; IPR036849; Enolase-like_C_sf.
DR   InterPro; IPR029017; Enolase-like_N.
DR   InterPro; IPR029065; Enolase_C-like.
DR   InterPro; IPR013342; Mandelate_racemase_C.
DR   InterPro; IPR013341; Mandelate_racemase_N_dom.
DR   Pfam; PF13378; MR_MLE_C; 1.
DR   Pfam; PF02746; MR_MLE_N; 1.
DR   SMART; SM00922; MR_MLE; 1.
DR   SUPFAM; SSF51604; SSF51604; 1.
DR   SUPFAM; SSF54826; SSF54826; 1.
PE   3: Inferred from homology;
KW   Isomerase; Magnesium; Metal-binding; Reference proteome.
FT   CHAIN           1..354
FT                   /note="L-Lys-D/L-Arg epimerase"
FT                   /id="PRO_0000429656"
FT   BINDING         135
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         160..162
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         190
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         215
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         240
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         265
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         295
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         318..320
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   354 AA;  38559 MW;  78412F41B6B28F08 CRC64;
     MKIKEITIWK EDLALTRPYT IAYETISAVE NVFVLLETDN GITGIGAGSP AEDVTGETIT
     ATETALSLKL APILQGKDIR SCFSLLKELN TALADTPAAL AAADIALHDL AAKTMGLPLV
     DLLGRVHDRL PTSITIGIMP VKETLAEAEE YLGRGFSILK IKTGLNVEED IERIIRLNET
     FKSKICMRVD ANQGYEVEEL HHFFKKTVGL VEFIEQPLKA EHLEKMGQLP QAIRRVSAAD
     ETLLGPRDAA QMLHAPRPFG IFNIKLMKCG GIAPGLEIAN MAGHADIDLM WGCMDESIVS
     IAGALHAAFS SRATRYLDLD GSLDLARDIV NGGFILENGW MRTTDQPGLG VKRI