AEEP_BACSU
ID AEEP_BACSU Reviewed; 366 AA.
AC O34508; Q796M5;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=L-Ala-D/L-Glu epimerase;
DE Short=AE epimerase;
DE Short=AEE;
DE EC=5.1.1.20 {ECO:0000269|PubMed:11747447};
GN Name=ykfB; OrderedLocusNames=BSU12980;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Devine K.M.;
RT "Sequence of the Bacillus subtilis genome between xlyA and ykoR.";
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND PROBABLE ROLE IN MUREIN PEPTIDE METABOLISM.
RC STRAIN=168;
RX PubMed=11747447; DOI=10.1021/bi011640x;
RA Schmidt D.M.Z., Hubbard B.K., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: functional
RT assignment of unknown proteins in Bacillus subtilis and Escherichia coli as
RT L-Ala-D/L-Glu epimerases.";
RL Biochemistry 40:15707-15715(2001).
RN [4]
RP INDUCTION.
RX PubMed=15101989; DOI=10.1111/j.1365-2958.2004.04023.x;
RA Hamon M.A., Stanley N.R., Britton R.A., Grossman A.D., Lazazzera B.A.;
RT "Identification of AbrB-regulated genes involved in biofilm formation by
RT Bacillus subtilis.";
RL Mol. Microbiol. 52:847-860(2004).
RN [5]
RP PROBABLE FUNCTION IN PEPTIDOGLYCAN DEGRADATION, AND REVIEW.
RX PubMed=18535144; DOI=10.1128/mmbr.00027-07;
RA Park J.T., Uehara T.;
RT "How bacteria consume their own exoskeletons (turnover and recycling of
RT cell wall peptidoglycan).";
RL Microbiol. Mol. Biol. Rev. 72:211-227(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR,
RP AND SUBUNIT.
RC STRAIN=168;
RX PubMed=11747448; DOI=10.1021/bi011641p;
RA Gulick A.M., Schmidt D.M.Z., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the enolase superfamily: crystal
RT structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and
RT Bacillus subtilis.";
RL Biochemistry 40:15716-15724(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
RP MAGNESIUM, COFACTOR, ACTIVE SITES, AND REACTION MECHANISM.
RC STRAIN=168;
RX PubMed=15301535; DOI=10.1021/bi049197o;
RA Klenchin V.A., Schmidt D.M.Z., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the enolase superfamily: structure of
RT a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus
RT subtilis.";
RL Biochemistry 43:10370-10378(2004).
CC -!- FUNCTION: Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and
CC has probably a role in the metabolism of the murein peptide, of which
CC L-Ala-D-Glu is a component. Is also able to catalyze the reverse
CC reaction and the epimerization of the other Ala-X dipeptides L-Ala-L-
CC Asp, L-Ala-L-Leu, L-Ala-L-Met, and L-Ala-L-Ser. Is not able to
CC epimerize other L-Ala-X dipeptides. Is also active with L-Ser-L-Glu
CC and, oddly, L-Pro-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Lys-
CC L-Ala, or D-Ala-D-Ala. {ECO:0000269|PubMed:11747447}.
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; Evidence={ECO:0000269|PubMed:11747447};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11747448, ECO:0000269|PubMed:15301535};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:11747448,
CC ECO:0000269|PubMed:15301535};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=320 uM for L-Ala-D-Glu (at pH 8.5) {ECO:0000269|PubMed:11747447};
CC KM=28 uM for L-Ala-D-Asp (at pH 8.5) {ECO:0000269|PubMed:11747447};
CC KM=510 uM for L-Ala-D-Met (at pH 8.5) {ECO:0000269|PubMed:11747447};
CC Note=The catalytic efficiency is 25-fold higher with L-Ala-D-Glu than
CC with L-Ala-D-Asp or L-Ala-D-Met as substrate.;
CC -!- PATHWAY: Cell wall degradation; peptidoglycan degradation.
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000269|PubMed:11747448,
CC ECO:0000269|PubMed:15301535}.
CC -!- INDUCTION: Repressed by AbrB, a transcription factor that negatively
CC controls biofilm formation. {ECO:0000269|PubMed:15101989}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AJ002571; CAA05578.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13155.1; -; Genomic_DNA.
DR PIR; H69855; H69855.
DR RefSeq; NP_389181.1; NC_000964.3.
DR RefSeq; WP_003244980.1; NZ_JNCM01000035.1.
DR PDB; 1JPM; X-ray; 2.25 A; A/B/C/D=1-366.
DR PDB; 1TKK; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-366.
DR PDBsum; 1JPM; -.
DR PDBsum; 1TKK; -.
DR AlphaFoldDB; O34508; -.
DR SMR; O34508; -.
DR STRING; 224308.BSU12980; -.
DR PaxDb; O34508; -.
DR EnsemblBacteria; CAB13155; CAB13155; BSU_12980.
DR GeneID; 939862; -.
DR KEGG; bsu:BSU12980; -.
DR PATRIC; fig|224308.179.peg.1410; -.
DR eggNOG; COG4948; Bacteria.
DR InParanoid; O34508; -.
DR OMA; MFGCYSD; -.
DR PhylomeDB; O34508; -.
DR BioCyc; BSUB:BSU12980-MON; -.
DR BRENDA; 5.1.1.20; 658.
DR SABIO-RK; O34508; -.
DR UniPathway; UPA00549; -.
DR EvolutionaryTrace; O34508; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0103031; F:L-Ala-D/L-Glu epimerase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016998; P:cell wall macromolecule catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
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 SFLD; SFLDF00010; dipeptide_epimerase; 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; Cell wall biogenesis/degradation; Isomerase; Magnesium;
KW Metal-binding; Reference proteome.
FT CHAIN 1..366
FT /note="L-Ala-D/L-Glu epimerase"
FT /id="PRO_0000388970"
FT ACT_SITE 162
FT /note="Proton acceptor; specific for (R)-substrate
FT epimerization"
FT /evidence="ECO:0000269|PubMed:15301535"
FT ACT_SITE 268
FT /note="Proton acceptor; specific for (S)-substrate
FT epimerization"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 24
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 160
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11747448,
FT ECO:0000269|PubMed:15301535"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11747448,
FT ECO:0000269|PubMed:15301535"
FT BINDING 244
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11747448,
FT ECO:0000269|PubMed:15301535"
FT BINDING 296
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 298
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 321
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT BINDING 323
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15301535"
FT STRAND 2..20
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 25..38
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:1TKK"
FT TURN 52..55
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 59..68
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 70..74
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 82..91
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 97..114
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 119..123
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 128..132
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 141..154
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:1JPM"
FT HELIX 168..182
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 184..191
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 275..287
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 301..313
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 317..320
FT /evidence="ECO:0007829|PDB:1TKK"
FT HELIX 324..327
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 333..336
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 338..340
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 349..351
FT /evidence="ECO:0007829|PDB:1TKK"
FT STRAND 354..357
FT /evidence="ECO:0007829|PDB:1TKK"
SQ SEQUENCE 366 AA; 39473 MW; 8E33E7955435CE8B CRC64;
MKIIRIETSR IAVPLTKPFK TALRTVYTAE SVIVRITYDS GAVGWGEAPP TLVITGDSMD
SIESAIHHVL KPALLGKSLA GYEAILHDIQ HLLTGNMSAK AAVEMALYDG WAQMCGLPLY
QMLGGYRDTL ETDYTVSVNS PEEMAADAEN YLKQGFQTLK IKVGKDDIAT DIARIQEIRK
RVGSAVKLRL DANQGWRPKE AVTAIRKMED AGLGIELVEQ PVHKDDLAGL KKVTDATDTP
IMADESVFTP RQAFEVLQTR SADLINIKLM KAGGISGAEK INAMAEACGV ECMVGSMIET
KLGITAAAHF AASKRNITRF DFDAPLMLKT DVFNGGITYS GSTISMPGKP GLGIIGAALL
KGEKEQ
