XEEP_FRAP2
ID XEEP_FRAP2 Reviewed; 356 AA.
AC B0TZW0;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 08-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=L-amino acid-D/L-Glu epimerase;
DE EC=5.1.1.-;
DE AltName: Full=L-Xxx-D/L-Glu epimerase;
GN OrderedLocusNames=Fphi_1647;
OS Francisella philomiragia subsp. philomiragia (strain ATCC 25017 / FSC 153 /
OS O#319-036).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales;
OC Francisellaceae; Francisella.
OX NCBI_TaxID=484022;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25017 / FSC 153 / O#319-036;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Richardson P.;
RT "Complete sequence of chromosome of Francisella philomiragia subsp.
RT philomiragia ATCC 25017.";
RL Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-356 IN COMPLEXES WITH DIPEPTIDE
RP AND MAGNESIUM, FUNCTION, AND COFACTOR.
RC STRAIN=ATCC 25017 / FSC 153 / O#319-036;
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 dipeptides with L-Glu in the
CC second position. Has epimerase activity with L-Ala-L-Glu, L-Pro-L-Glu,
CC L-Val-L-Glu, L-Thr-L-Glu and L-Met-L-Glu (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; CP000937; ABZ87872.1; -; Genomic_DNA.
DR RefSeq; WP_012280945.1; NC_010336.1.
DR PDB; 3R0K; X-ray; 2.00 A; A/B=2-356.
DR PDB; 3R0U; X-ray; 1.90 A; A/B=2-356.
DR PDB; 3R10; X-ray; 2.00 A; A/B=2-356.
DR PDB; 3R11; X-ray; 2.00 A; A/B=2-356.
DR PDB; 3R1Z; X-ray; 1.90 A; A/B=2-356.
DR PDBsum; 3R0K; -.
DR PDBsum; 3R0U; -.
DR PDBsum; 3R10; -.
DR PDBsum; 3R11; -.
DR PDBsum; 3R1Z; -.
DR AlphaFoldDB; B0TZW0; -.
DR SMR; B0TZW0; -.
DR STRING; 484022.Fphi_1647; -.
DR EnsemblBacteria; ABZ87872; ABZ87872; Fphi_1647.
DR KEGG; fph:Fphi_1647; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_0_6; -.
DR OMA; HEEFPVT; -.
DR EvolutionaryTrace; B0TZW0; -.
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: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 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Metal-binding.
FT CHAIN 1..356
FT /note="L-amino acid-D/L-Glu epimerase"
FT /id="PRO_0000429659"
FT BINDING 25
FT /ligand="substrate"
FT BINDING 136
FT /ligand="substrate"
FT BINDING 161..163
FT /ligand="substrate"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 193
FT /ligand="substrate"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 244
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 268
FT /ligand="substrate"
FT BINDING 296..298
FT /ligand="substrate"
FT BINDING 320..322
FT /ligand="substrate"
FT STRAND 3..21
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 26..39
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 44..50
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 53..56
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 60..69
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 83..91
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 98..115
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 142..154
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 168..181
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 198..209
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 275..287
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 301..313
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 322..326
FT /evidence="ECO:0007829|PDB:3R0U"
FT HELIX 329..331
FT /evidence="ECO:0007829|PDB:3R0U"
FT TURN 332..335
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 336..339
FT /evidence="ECO:0007829|PDB:3R0U"
FT STRAND 342..345
FT /evidence="ECO:0007829|PDB:3R0U"
SQ SEQUENCE 356 AA; 39071 MW; F10371B923FDEBEB CRC64;
MSKIIDIKTS IIKIPLKRTF ITAVRSTNHI DSLAVELTLD NGVKGYGVAP ATTAITGDTL
QGMQYIIREI FAPVILGSDL SDYKQTLELA FKKVMFNSAA KMAIDLAYHD LLAKEQDISV
AKLLGAKANS IVTDVSISCG NVAETIQNIQ NGVEANFTAI KVKTGADFNR DIQLLKALDN
EFSKNIKFRF DANQGWNLAQ TKQFIEEINK YSLNVEIIEQ PVKYYDIKAM AEITKFSNIP
VVADESVFDA KDAERVIDEQ ACNMINIKLA KTGGILEAQK IKKLADSAGI SCMVGCMMES
PAGILATASF ALAEDITVAD LDPLDWVAKD LYSDYITFNE PNIILKDNLK GFGFNL
