AEEP_BACTN
ID AEEP_BACTN Reviewed; 383 AA.
AC Q8A861;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=L-Ala-D/L-Glu epimerase;
DE Short=AE epimerase;
DE Short=AEE;
DE EC=5.1.1.20;
GN OrderedLocusNames=BT_1313;
OS Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 /
OS CCUG 10774 / NCTC 10582 / VPI-5482 / E50).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=226186;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=12663928; DOI=10.1126/science.1080029;
RA Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C.,
RA Hooper L.V., Gordon J.I.;
RT "A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.";
RL Science 299:2074-2076(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=19321416; DOI=10.1073/pnas.0901529106;
RA Mahowald M.A., Rey F.E., Seedorf H., Turnbaugh P.J., Fulton R.S.,
RA Wollam A., Shah N., Wang C., Magrini V., Wilson R.K., Cantarel B.L.,
RA Coutinho P.M., Henrissat B., Crock L.W., Russell A., Verberkmoes N.C.,
RA Hettich R.L., Gordon J.I.;
RT "Characterizing a model human gut microbiota composed of members of its two
RT dominant bacterial phyla.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:5859-5864(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 46-383 IN COMPLEX WITH DIPEPTIDE
RP AND MAGNESIUM, COFACTOR, FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
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-Ala-D-Glu to L-Ala-L-Glu and
CC may play a role in the metabolism of the murein peptide, of which L-
CC Ala-D-Glu is a component. Is also able to catalyze the epimerization of
CC L-Ala-D-Asp, L-Ala-L-Glu, L-Ala-L-Ser, L-Ala-L-Pro, L-Ala-L-L-Val, L-
CC Ala-L-Thr, L-Ala-L-Leu, L-Ala-L-Ile and L-Gly-L-Glu (in vitro).
CC {ECO:0000269|PubMed:22392983}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-alanyl-L-glutamate = L-alanyl-D-glutamate;
CC Xref=Rhea:RHEA:28394, ChEBI:CHEBI:61395, ChEBI:CHEBI:61396;
CC EC=5.1.1.20;
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=2.0 mM for L-Ala-L-Glu {ECO:0000269|PubMed:22392983};
CC KM=6.0 mM for L-Ala-D-Glu {ECO:0000269|PubMed:22392983};
CC KM=1.7 mM for L-Val-L-Glu {ECO:0000269|PubMed:22392983};
CC KM=4.4 mM for L-Val-D-Glu {ECO:0000269|PubMed:22392983};
CC Note=kcat is 147 sec(-1) for epimerization of L-Ala-L-Glu. kcat is 59
CC sec(-1) for epimerization of L-Ala-D-Glu. kcat is 96 sec(-1) for
CC epimerization of L-Val-L-Glu. kcat is 43 sec(-1) for epimerization of
CC L-Val-D-Glu. kcat is 30 sec(-1) for epimerization of L-Ile-L-Glu.;
CC -!- MISCELLANEOUS: Part of a large, functionally divergent protein family.
CC Protein modeling and substrate docking were 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; AE015928; AAO76420.1; -; Genomic_DNA.
DR RefSeq; NP_810226.1; NC_004663.1.
DR RefSeq; WP_011107704.1; NC_004663.1.
DR PDB; 3IJI; X-ray; 1.60 A; A/B=46-383.
DR PDB; 3IJL; X-ray; 1.50 A; A/B=46-383.
DR PDB; 3IJQ; X-ray; 2.00 A; A/B=46-383.
DR PDBsum; 3IJI; -.
DR PDBsum; 3IJL; -.
DR PDBsum; 3IJQ; -.
DR AlphaFoldDB; Q8A861; -.
DR SMR; Q8A861; -.
DR STRING; 226186.BT_1313; -.
DR PaxDb; Q8A861; -.
DR PRIDE; Q8A861; -.
DR EnsemblBacteria; AAO76420; AAO76420; BT_1313.
DR GeneID; 60927293; -.
DR KEGG; bth:BT_1313; -.
DR PATRIC; fig|226186.12.peg.1342; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_3_10; -.
DR InParanoid; Q8A861; -.
DR OMA; DIVDHRH; -.
DR Proteomes; UP000001414; Chromosome.
DR GO; GO:0103031; F:L-Ala-D/L-Glu epimerase activity; IEA:RHEA.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0016854; F:racemase and epimerase activity; IDA:UniProtKB.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
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; IPR034593; Mandelate_racemase_DgoD-like.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR InterPro; IPR006311; TAT_signal.
DR InterPro; IPR019546; TAT_signal_bac_arc.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00010; dipeptide_epimerase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR TIGRFAMs; TIGR01409; TAT_signal_seq; 1.
DR PROSITE; PS51318; TAT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Isomerase; Magnesium;
KW Metal-binding; Reference proteome.
FT CHAIN 1..383
FT /note="L-Ala-D/L-Glu epimerase"
FT /id="PRO_0000429646"
FT BINDING 68
FT /ligand="substrate"
FT BINDING 94
FT /ligand="substrate"
FT BINDING 198..200
FT /ligand="substrate"
FT BINDING 224
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 251
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22392983"
FT BINDING 298
FT /ligand="substrate"
FT BINDING 326..328
FT /ligand="substrate"
FT BINDING 348..350
FT /ligand="substrate"
FT STRAND 48..52
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 55..63
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 83..90
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 93..95
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 99..106
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 120..129
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 135..153
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 165..167
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 180..191
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 195..200
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 206..214
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 221..224
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 232..244
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 247..251
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:3IJI"
FT HELIX 259..267
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 273..276
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:3IJL"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:3IJQ"
FT STRAND 292..297
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 299..302
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 305..317
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 321..324
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 331..338
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 339..343
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:3IJL"
FT HELIX 351..354
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 364..366
FT /evidence="ECO:0007829|PDB:3IJL"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:3IJL"
SQ SEQUENCE 383 AA; 42168 MW; 1088235F1C0A356F CRC64;
MPNRRDFLKT AAFATLGSGI AVSQVLAGEC MPSAIHINKY GIGGKMKMTF FPYELKLRHV
FTVATYSRTT TPDVQVEIEY EGVTGYGEAS MPPYLGETVE SVMNFLKKVN LEQFSDPFQL
EDILSYVDSL SPKDTAAKAA VDIALHDLVG KLLGAPWYKI WGLNKEKTPS TTFTIGIDTP
DVVRAKTKEC AGLFNILKVK LGRDNDKEMI ETIRSVTDLP IAVDANQGWK DRQYALDMIH
WLKEKGIVMI EQPMPKEQLD DIAWVTQQSP LPVFADESLQ RLGDVAALKG AFTGINIKLM
KCTGMREAWK MVTLAHALGM RVMVGCMTET SCAISAASQF SPAVDFADLD GNLLISNDRF
KGVEVVNGKI TLNDLPGIGV MKI
