AXEP_POPTR
ID AXEP_POPTR Reviewed; 421 AA.
AC B9I2J6;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 11-DEC-2013, sequence version 2.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=L-Ala-D/L-amino acid epimerase;
DE EC=5.1.1.-;
DE AltName: Full=L-Ala-D/L-Xxx epimerase;
GN ORFNames=POPTR_0012s05040g;
OS Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp.
OS trichocarpa).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus.
OX NCBI_TaxID=3694;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nisqually;
RX PubMed=16973872; DOI=10.1126/science.1128691;
RA Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I.,
RA Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J.,
RA Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W.,
RA Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M.,
RA Chapman J., Chen G.-L., Cooper D., Coutinho P.M., Couturier J., Covert S.,
RA Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A.,
RA dePamphilis C.W., Detter J., Dirks B., Dubchak I., Duplessis S.,
RA Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J.,
RA Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y.,
RA Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S.,
RA Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjaervi J., Karlsson J.,
RA Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F.,
RA Leebens-Mack J., Leple J.-C., Locascio P., Lou Y., Lucas S., Martin F.,
RA Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O.,
RA Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J.,
RA Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J.,
RA Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A.,
RA Tsai C.-J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S.,
RA Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y.,
RA Rokhsar D.S.;
RT "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).";
RL Science 313:1596-1604(2006).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nisqually;
RG US DOE Joint Genome Institute (JGI-PGF);
RA Grigoriev I.V., Terry A., Salamov A.A., Otillar R., Lou Y., Lucas S.,
RA Hammon N., Glavina del Rio T., Detter J., Kalin E., Tice H., Pitluck S.,
RA Chapman J., Putnam N.H., Brunner A., Busov V., Campbell M., Chalot M.,
RA Covert S., Davis J., DiFazio S., Gribskov M., Gunter L., Hamberger B.,
RA Jansson S., Joshi C., Larimer F., Martin F., Napoli C., Nelson D.,
RA Ralph S., Rombauts S., Rouze P., Schrader J., Tsai C., Vahala J.,
RA Tuskan G., Rokhsar D.;
RL Submitted (DEC-2008) to the EMBL/GenBank/DDBJ databases.
RN [3]
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 various hydrophobic and polar
CC dipeptides. Has epimerase activity with L-Ala-L-Ala, L-Ala-L-Ser, L-
CC Ala-L-Thr and L-Ala-L-Trp (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 -!- 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; CM009301; EEE96122.2; -; Genomic_DNA.
DR RefSeq; XP_002317902.2; XM_002317866.2.
DR AlphaFoldDB; B9I2J6; -.
DR SMR; B9I2J6; -.
DR STRING; 3694.POPTR_0012s05040.1; -.
DR EnsemblPlants; PNT09601; PNT09601; POPTR_012G054200v3.
DR EnsemblPlants; PNT09603; PNT09603; POPTR_012G054200v3.
DR EnsemblPlants; PNT09604; PNT09604; POPTR_012G054200v3.
DR GeneID; 7493512; -.
DR Gramene; PNT09601; PNT09601; POPTR_012G054200v3.
DR Gramene; PNT09603; PNT09603; POPTR_012G054200v3.
DR Gramene; PNT09604; PNT09604; POPTR_012G054200v3.
DR KEGG; pop:7493512; -.
DR eggNOG; ENOG502QU7C; Eukaryota.
DR HOGENOM; CLU_030273_4_1_1; -.
DR InParanoid; B9I2J6; -.
DR OMA; MFGCYSD; -.
DR Proteomes; UP000006729; Chromosome 12.
DR ExpressionAtlas; B9I2J6; baseline and differential.
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 3: Inferred from homology;
KW Isomerase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..421
FT /note="L-Ala-D/L-amino acid epimerase"
FT /id="PRO_0000429650"
FT BINDING 193
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 218..220
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 304
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 328
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 380..382
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 421 AA; 45553 MW; F7C6DC409EA9DABE CRC64;
MLSIGSLCLS LGTTPKPLKP SKTPKPIRKL YATKAMAGSN PKQVSTFEFR DLMETFAVDV
KRAENRPLNV PLIAPFTIAS SRLDKVENVA IRIELSDGCV GWGEAPILPF VTAEDQSTAM
IKAREACELL KNSSSMKLGL VLERVSEILP GHEFASVRAG VEMALIDAVA KSINVPLWIL
FGGASDSITT DITIPIVSSA EAAELASKYR KQGFQTLKLK VGKNLKEDIE VLQAIRAVHP
DCLFILDANE GYKPEEAIEV LEELHKMGVT PILFEQPVHR DDWEGLGHVT HIAKGKYGVS
VAADESCRSL VDAKRIIKGN LADVINIKLA KVGVVGGLEI IEEARTSGLD LMIGGMVETR
LAMGFAGHLA AGFGCFKFID LDTPLLLSED PVLEGYEVSG AVYKFTDAQG HAGFLDWDNV
L
