KRDE_METCA
ID KRDE_METCA Reviewed; 356 AA.
AC Q607C7;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=L-Lys-D/L-Arg epimerase;
DE EC=5.1.1.-;
DE AltName: Full=Cationic dipeptide epimerase;
GN OrderedLocusNames=MCA1834;
OS Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Methylococcales;
OC Methylococcaceae; Methylococcus.
OX NCBI_TaxID=243233;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33009 / NCIMB 11132 / Bath;
RX PubMed=15383840; DOI=10.1371/journal.pbio.0020303;
RA Ward N.L., Larsen O., Sakwa J., Bruseth L., Khouri H.M., Durkin A.S.,
RA Dimitrov G., Jiang L., Scanlan D., Kang K.H., Lewis M.R., Nelson K.E.,
RA Methe B.A., Wu M., Heidelberg J.F., Paulsen I.T., Fouts D.E., Ravel J.,
RA Tettelin H., Ren Q., Read T.D., DeBoy R.T., Seshadri R., Salzberg S.L.,
RA Jensen H.B., Birkeland N.K., Nelson W.C., Dodson R.J., Grindhaug S.H.,
RA Holt I.E., Eidhammer I., Jonasen I., Vanaken S., Utterback T.R.,
RA Feldblyum T.V., Fraser C.M., Lillehaug J.R., Eisen J.A.;
RT "Genomic insights into methanotrophy: the complete genome sequence of
RT Methylococcus capsulatus (Bath).";
RL PLoS Biol. 2:1616-1628(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF APOPROTEIN AND IN COMPLEX WITH
RP MAGNESIUM AND L-ARG-D-LYS DIPEPTIDE, FUNCTION, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
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.
CC Can also catalyze the epimerization of other cationic dipeptides, such
CC as L-Arg-L-Arg, L-Lys-L-Lys and L-Lys-L-His, but with lower efficiency
CC (in vitro). {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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.15 mM for L-Lys-L-Lys {ECO:0000269|PubMed:22392983};
CC KM=0.19 mM for L-Arg-L-Arg {ECO:0000269|PubMed:22392983};
CC KM=0.44 mM for L-Lys-L-Arg {ECO:0000269|PubMed:22392983};
CC KM=0.88 mM for L-Lys-L-His {ECO:0000269|PubMed:22392983};
CC Note=kcat is 8.4 sec(-1) for epimerization of L-Lys-L-Arg. kcat is
CC 0.029 sec(-1) for epimerization of L-Lys-L-Lys. kcat is 0.72 sec(-1)
CC for epimerization of L-Arg-L-Arg.;
CC -!- MISCELLANEOUS: Part of a large, functionally divergent protein family.
CC Was initially predicted to have chloromuconate cycloisomerase activity,
CC based on sequence similarity. Protein modeling and substrate docking
CC was used to predict the substrate specificity, prior to biochemical
CC analysis (PubMed:22392983). {ECO:0000305|PubMed:22392983}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AE017282; AAU91952.1; -; Genomic_DNA.
DR RefSeq; WP_010961086.1; NC_002977.6.
DR PDB; 3RIT; X-ray; 2.70 A; A/B/C/D/E=1-356.
DR PDB; 3RO6; X-ray; 2.20 A; A/B/C/D/E/F=1-356.
DR PDBsum; 3RIT; -.
DR PDBsum; 3RO6; -.
DR AlphaFoldDB; Q607C7; -.
DR SMR; Q607C7; -.
DR STRING; 243233.MCA1834; -.
DR DNASU; 3103133; -.
DR EnsemblBacteria; AAU91952; AAU91952; MCA1834.
DR KEGG; mca:MCA1834; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_0_6; -.
DR OMA; MFGCYSD; -.
DR OrthoDB; 951991at2; -.
DR Proteomes; UP000006821; Chromosome.
DR GO; GO:0018850; F:chloromuconate cycloisomerase activity; ISS:JCVI.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
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:0019614; P:catechol-containing compound catabolic process; ISS:JCVI.
DR GO; GO:0009063; P:cellular amino acid catabolic process; 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; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
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.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..356
FT /note="L-Lys-D/L-Arg epimerase"
FT /id="PRO_0000429657"
FT BINDING 135
FT /ligand="substrate"
FT BINDING 160..162
FT /ligand="substrate"
FT BINDING 190
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 216
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 266
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 296
FT /ligand="substrate"
FT BINDING 319..321
FT /ligand="substrate"
FT STRAND 2..15
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 28..38
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:3RO6"
FT TURN 72..76
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 82..92
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 97..115
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 119..122
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 141..153
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 167..181
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 184..190
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 197..209
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 224..228
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 232..236
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 247..254
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 261..265
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 267..270
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 273..286
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 289..292
FT /evidence="ECO:0007829|PDB:3RO6"
FT HELIX 299..310
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:3RO6"
FT TURN 322..325
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:3RO6"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:3RO6"
SQ 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
