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L-Lys-D/L-Arg epimerase (EC 5.1.1.-) (Cationic dipeptide epimerase)

 KRDE_METCA              Reviewed;         356 AA.
Q607C7;
09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
23-NOV-2004, sequence version 1.
28-FEB-2018, entry version 76.
RecName: Full=L-Lys-D/L-Arg epimerase;
EC=5.1.1.-;
AltName: Full=Cationic dipeptide epimerase;
OrderedLocusNames=MCA1834;
Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath).
Bacteria; Proteobacteria; Gammaproteobacteria; Methylococcales;
Methylococcaceae; Methylococcus.
NCBI_TaxID=243233;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 33009 / NCIMB 11132 / Bath;
PubMed=15383840; DOI=10.1371/journal.pbio.0020303;
Ward N.L., Larsen O., Sakwa J., Bruseth L., Khouri H.M., Durkin A.S.,
Dimitrov G., Jiang L., Scanlan D., Kang K.H., Lewis M.R., Nelson K.E.,
Methe B.A., Wu M., Heidelberg J.F., Paulsen I.T., Fouts D.E.,
Ravel J., Tettelin H., Ren Q., Read T.D., DeBoy R.T., Seshadri R.,
Salzberg S.L., Jensen H.B., Birkeland N.K., Nelson W.C., Dodson R.J.,
Grindhaug S.H., Holt I.E., Eidhammer I., Jonasen I., Vanaken S.,
Utterback T.R., Feldblyum T.V., Fraser C.M., Lillehaug J.R.,
Eisen J.A.;
"Genomic insights into methanotrophy: the complete genome sequence of
Methylococcus capsulatus (Bath).";
PLoS Biol. 2:1616-1628(2004).
[2]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF APOPROTEIN AND IN COMPLEX
WITH MAGNESIUM AND L-ARG-D-LYS DIPEPTIDE, FUNCTION, COFACTOR, AND
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=22392983; DOI=10.1073/pnas.1112081109;
Lukk T., Sakai A., Kalyanaraman C., Brown S.D., Imker H.J., Song L.,
Fedorov A.A., Fedorov E.V., Toro R., Hillerich B., Seidel R.,
Patskovsky Y., Vetting M.W., Nair S.K., Babbitt P.C., Almo S.C.,
Gerlt J.A., Jacobson M.P.;
"Homology models guide discovery of diverse enzyme specificities among
dipeptide epimerases in the enolase superfamily.";
Proc. Natl. Acad. Sci. U.S.A. 109:4122-4127(2012).
-!- FUNCTION: Catalyzes the epimerization of L-Lys-L-Arg to L-Lys-D-
Arg. Can also catalyze the epimerization of other cationic
dipeptides, such as L-Arg-L-Arg, L-Lys-L-Lys and L-Lys-L-His, but
with lower efficiency (in vitro). {ECO:0000269|PubMed:22392983}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:22392983};
Note=Binds 1 Mg(2+) ion per subunit.
{ECO:0000269|PubMed:22392983};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.15 mM for L-Lys-L-Lys {ECO:0000269|PubMed:22392983};
KM=0.19 mM for L-Arg-L-Arg {ECO:0000269|PubMed:22392983};
KM=0.44 mM for L-Lys-L-Arg {ECO:0000269|PubMed:22392983};
KM=0.88 mM for L-Lys-L-His {ECO:0000269|PubMed:22392983};
Note=kcat is 8.4 sec(-1) for epimerization of L-Lys-L-Arg. kcat
is 0.029 sec(-1) for epimerization of L-Lys-L-Lys. kcat is 0.72
sec(-1) for epimerization of L-Arg-L-Arg.;
-!- MISCELLANEOUS: Part of a large, functionally divergent protein
family. Was initially predicted to have chloromuconate
cycloisomerase activity, based on sequence similarity. Protein
modeling and substrate docking was used to predict the substrate
specificity, prior to biochemical analysis (PubMed:22392983).
{ECO:0000305|PubMed:22392983}.
-!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
enzyme family. {ECO:0000305}.
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EMBL; AE017282; AAU91952.1; -; Genomic_DNA.
RefSeq; WP_010961086.1; NC_002977.6.
PDB; 3RIT; X-ray; 2.70 A; A/B/C/D/E=1-356.
PDB; 3RO6; X-ray; 2.20 A; A/B/C/D/E/F=1-356.
PDBsum; 3RIT; -.
PDBsum; 3RO6; -.
ProteinModelPortal; Q607C7; -.
SMR; Q607C7; -.
STRING; 243233.MCA1834; -.
DNASU; 3103133; -.
EnsemblBacteria; AAU91952; AAU91952; MCA1834.
KEGG; mca:MCA1834; -.
eggNOG; ENOG4107S8C; Bacteria.
eggNOG; COG4948; LUCA.
HOGENOM; HOG000185903; -.
OMA; CYSDSSL; -.
OrthoDB; POG091H04PO; -.
BioCyc; MCAP243233:G1G0X-1822-MONOMER; -.
Proteomes; UP000006821; Chromosome.
GO; GO:0018850; F:chloromuconate cycloisomerase activity; ISS:JCVI.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0016854; F:racemase and epimerase activity; IDA:UniProtKB.
GO; GO:0019614; P:catechol-containing compound catabolic process; ISS:JCVI.
GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
GO; GO:0006518; P:peptide metabolic process; IDA:UniProtKB.
Gene3D; 3.20.20.120; -; 1.
Gene3D; 3.30.390.10; -; 1.
InterPro; IPR036849; Enolase-like_C_sf.
InterPro; IPR029017; Enolase-like_N.
InterPro; IPR034390; Enolase-like_superfamily.
InterPro; IPR029065; Enolase_C-like.
InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
InterPro; IPR013342; Mandelate_racemase_C.
InterPro; IPR013341; Mandelate_racemase_N_dom.
Pfam; PF13378; MR_MLE_C; 1.
Pfam; PF02746; MR_MLE_N; 1.
SFLD; SFLDS00001; Enolase; 1.
SMART; SM00922; MR_MLE; 1.
SUPFAM; SSF51604; SSF51604; 1.
PROSITE; PS00909; MR_MLE_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Isomerase; Magnesium; Metal-binding;
Reference proteome.
CHAIN 1 356 L-Lys-D/L-Arg epimerase.
/FTId=PRO_0000429657.
REGION 160 162 Substrate binding.
REGION 319 321 Substrate binding.
METAL 190 190 Magnesium. {ECO:0000269|PubMed:22392983}.
METAL 216 216 Magnesium. {ECO:0000269|PubMed:22392983}.
METAL 241 241 Magnesium. {ECO:0000269|PubMed:22392983}.
BINDING 135 135 Substrate.
BINDING 266 266 Substrate. {ECO:0000250}.
BINDING 296 296 Substrate.
STRAND 2 15 {ECO:0000244|PDB:3RO6}.
STRAND 28 38 {ECO:0000244|PDB:3RO6}.
STRAND 43 48 {ECO:0000244|PDB:3RO6}.
HELIX 52 55 {ECO:0000244|PDB:3RO6}.
HELIX 59 66 {ECO:0000244|PDB:3RO6}.
HELIX 68 70 {ECO:0000244|PDB:3RO6}.
TURN 72 76 {ECO:0000244|PDB:3RO6}.
HELIX 79 81 {ECO:0000244|PDB:3RO6}.
HELIX 82 92 {ECO:0000244|PDB:3RO6}.
HELIX 97 115 {ECO:0000244|PDB:3RO6}.
HELIX 119 122 {ECO:0000244|PDB:3RO6}.
STRAND 130 132 {ECO:0000244|PDB:3RO6}.
STRAND 134 136 {ECO:0000244|PDB:3RO6}.
HELIX 141 153 {ECO:0000244|PDB:3RO6}.
STRAND 158 162 {ECO:0000244|PDB:3RO6}.
HELIX 167 181 {ECO:0000244|PDB:3RO6}.
STRAND 184 190 {ECO:0000244|PDB:3RO6}.
HELIX 197 209 {ECO:0000244|PDB:3RO6}.
HELIX 224 228 {ECO:0000244|PDB:3RO6}.
HELIX 232 236 {ECO:0000244|PDB:3RO6}.
STRAND 238 241 {ECO:0000244|PDB:3RO6}.
HELIX 247 254 {ECO:0000244|PDB:3RO6}.
STRAND 255 257 {ECO:0000244|PDB:3RO6}.
STRAND 261 265 {ECO:0000244|PDB:3RO6}.
HELIX 267 270 {ECO:0000244|PDB:3RO6}.
HELIX 273 286 {ECO:0000244|PDB:3RO6}.
STRAND 289 292 {ECO:0000244|PDB:3RO6}.
HELIX 299 310 {ECO:0000244|PDB:3RO6}.
STRAND 315 318 {ECO:0000244|PDB:3RO6}.
TURN 322 325 {ECO:0000244|PDB:3RO6}.
STRAND 332 334 {ECO:0000244|PDB:3RO6}.
STRAND 336 338 {ECO:0000244|PDB:3RO6}.
STRAND 341 343 {ECO:0000244|PDB:3RO6}.
STRAND 346 349 {ECO:0000244|PDB:3RO6}.
SEQUENCE 356 AA; 39039 MW; 2F27622703B3BA30 CRC64;
MKIADIQVRT EHFPLTRPYR IAFRSIEEID NLIVEIRTAD GLLGLGAASP ERHVTGETLE
ACHAALDHDR LGWLMGRDIR TLPRLCRELA ERLPAAPAAR AALDMALHDL VAQCLGLPLV
EILGRAHDSL PTSVTIGIKP VEETLAEARE HLALGFRVLK VKLCGDEEQD FERLRRLHET
LAGRAVVRVD PNQSYDRDGL LRLDRLVQEL GIEFIEQPFP AGRTDWLRAL PKAIRRRIAA
DESLLGPADA FALAAPPAAC GIFNIKLMKC GGLAPARRIA TIAETAGIDL MWGCMDESRI
SIAAALHAAL ACPATRYLDL DGSFDLARDV AEGGFILEDG RLRVTERPGL GLVYPD


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