AEEP_THEMA
ID AEEP_THEMA Reviewed; 345 AA.
AC Q9WXM1;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 111.
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, ECO:0000269|PubMed:19000819};
GN OrderedLocusNames=TM_0006;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP CATALYTIC ACTIVITY.
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 [3]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP SUBSTRATE AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=19000819; DOI=10.1016/j.str.2008.08.015;
RA Kalyanaraman C., Imker H.J., Fedorov A.A., Fedorov E.V., Glasner M.E.,
RA Babbitt P.C., Almo S.C., Gerlt J.A., Jacobson M.P.;
RT "Discovery of a dipeptide epimerase enzymatic function guided by homology
RT modeling and virtual screening.";
RL Structure 16:1668-1677(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of muconate cycloisomerase from Thermotoga maritima
RT MSB8.";
RL Submitted (FEB-2009) to the PDB data bank.
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 a broad range of other dipeptides; is
CC most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.
CC {ECO:0000269|PubMed:19000819}.
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 ECO:0000269|PubMed:19000819};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.8 mM for L-Ala-L-Glu (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=1.3 mM for L-Ala-L-Phe (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=0.71 mM for L-Ala-L-Tyr (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=5.3 mM for L-Ala-L-His (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=2.9 mM for L-Ala-L-Leu (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=4.7 mM for L-Ile-L-Phe (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC KM=3.9 mM for L-Lys-L-Phe (at pH 7.5 and 28 degrees Celsius)
CC {ECO:0000269|PubMed:19000819};
CC -!- PATHWAY: Cell wall degradation; peptidoglycan degradation.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AE000512; AAD35100.1; -; Genomic_DNA.
DR PIR; H72429; H72429.
DR RefSeq; NP_227822.1; NC_000853.1.
DR RefSeq; WP_004082436.1; NZ_CP011107.1.
DR PDB; 2ZAD; X-ray; 1.60 A; A/B/C/D=1-345.
DR PDB; 3DEQ; X-ray; 2.10 A; A/B/C/D=1-345.
DR PDB; 3DER; X-ray; 1.90 A; A/B/C/D=1-345.
DR PDB; 3DES; X-ray; 2.30 A; A/B/C/D=1-345.
DR PDB; 3DFY; X-ray; 2.10 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-345.
DR PDBsum; 2ZAD; -.
DR PDBsum; 3DEQ; -.
DR PDBsum; 3DER; -.
DR PDBsum; 3DES; -.
DR PDBsum; 3DFY; -.
DR AlphaFoldDB; Q9WXM1; -.
DR SMR; Q9WXM1; -.
DR STRING; 243274.THEMA_04770; -.
DR DNASU; 896814; -.
DR EnsemblBacteria; AAD35100; AAD35100; TM_0006.
DR KEGG; tma:TM0006; -.
DR eggNOG; COG4948; Bacteria.
DR InParanoid; Q9WXM1; -.
DR OMA; MFGCYSD; -.
DR OrthoDB; 951991at2; -.
DR SABIO-RK; Q9WXM1; -.
DR UniPathway; UPA00549; -.
DR EvolutionaryTrace; Q9WXM1; -.
DR Proteomes; UP000008183; 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:0016855; F:racemase and epimerase activity, acting on amino acids and derivatives; IDA:CACAO.
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 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..345
FT /note="L-Ala-D/L-Glu epimerase"
FT /id="PRO_0000388972"
FT ACT_SITE 161
FT /note="Proton acceptor; specific for (R)-substrate
FT epimerization"
FT /evidence="ECO:0000250"
FT ACT_SITE 265
FT /note="Proton acceptor; specific for (S)-substrate
FT epimerization"
FT /evidence="ECO:0000250"
FT BINDING 134
FT /ligand="substrate"
FT BINDING 159
FT /ligand="substrate"
FT BINDING 188
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 190
FT /ligand="substrate"
FT BINDING 216
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 292
FT /ligand="substrate"
FT BINDING 317
FT /ligand="substrate"
FT BINDING 319
FT /ligand="substrate"
FT STRAND 3..22
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 25..39
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 53..56
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 60..65
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 67..74
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 82..89
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 96..114
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 118..121
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 140..152
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 195..207
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 224..233
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 247..256
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 266..282
FT /evidence="ECO:0007829|PDB:2ZAD"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 297..310
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:2ZAD"
FT HELIX 320..323
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 332..336
FT /evidence="ECO:0007829|PDB:2ZAD"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:2ZAD"
SQ SEQUENCE 345 AA; 38664 MW; 587BDE71BB1E777B CRC64;
MSRIVNVKLS LKRYEYEKPF HITGSVSSES RNVEVEIVLE SGVKGYGEAS PSFRVNGERV
EALLAIENAV REMITGIDVR NYARIFEITD RLFGFPSLKA AVQFATLDAL SQELGTQVCY
LLGGKRDEIE TDKTVGIDTV ENRVKEAKKI FEEGFRVIKI KVGENLKEDI EAVEEIAKVT
RGAKYIVDAN MGYTQKEAVE FARAVYQKGI DIAVYEQPVR REDIEGLKFV RFHSPFPVAA
DESARTKFDV MRLVKEEAVD YVNIKLMKSG ISDALAIVEI AESSGLKLMI GCMGESSLGI
NQSVHFALGT GAFEFHDLDS HLMLKEEVFR GKFIQDGPRM RVKDQ
