AAEP_CYTH3
ID AAEP_CYTH3 Reviewed; 368 AA.
AC Q11T61;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=D-Ala-D/L-Ala epimerase;
DE EC=5.1.1.-;
GN Name=tfdD; OrderedLocusNames=CHU_2140;
OS Cytophaga hutchinsonii (strain ATCC 33406 / DSM 1761 / CIP 103989 / NBRC
OS 15051 / NCIMB 9469 / D465).
OC Bacteria; Bacteroidetes; Cytophagia; Cytophagales; Cytophagaceae;
OC Cytophaga.
OX NCBI_TaxID=269798;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33406 / DSM 1761 / CIP 103989 / NBRC 15051 / NCIMB 9469 / D465;
RX PubMed=17400776; DOI=10.1128/aem.00225-07;
RA Xie G., Bruce D.C., Challacombe J.F., Chertkov O., Detter J.C., Gilna P.,
RA Han C.S., Lucas S., Misra M., Myers G.L., Richardson P., Tapia R.,
RA Thayer N., Thompson L.S., Brettin T.S., Henrissat B., Wilson D.B.,
RA McBride M.J.;
RT "Genome sequence of the cellulolytic gliding bacterium Cytophaga
RT hutchinsonii.";
RL Appl. Environ. Microbiol. 73:3536-3546(2007).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM;
RP D-ALA-L-VAL AND D-ALA-L-ALA, FUNCTION, COFACTOR, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=ATCC 33406 / DSM 1761 / CIP 103989 / NBRC 15051 / NCIMB 9469 / D465;
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 D-Ala-D-Ala to D-Ala-L-Ala.
CC Has broad substrate specificity and catalyzes the epimerization of a
CC variety of dipeptides containing an N-terminal Ala followed by a
CC hydrophobic or polar residue, such as Val, Ser and Met (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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.1 mM for D-Ala-L-Ala {ECO:0000269|PubMed:22392983};
CC KM=1.9 mM for D-Ala-D-Ala {ECO:0000269|PubMed:22392983};
CC KM=0.5 mM for D-Ala-L-Val {ECO:0000269|PubMed:22392983};
CC KM=5.0 mM for L-Ala-L-Ala {ECO:0000269|PubMed:22392983};
CC Note=kcat is 43 sec(-1) for epimerization of D-Ala-D-Ala. kcat is 58
CC sec(-1) for epimerization of D-Ala-L-Ala. kcat is 19 sec(-1) for
CC epimerization of D-Ala-L-Val. kcat is 37 sec(-1) for epimerization of
CC L-Ala-L-Ala.;
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; CP000383; ABG59403.1; -; Genomic_DNA.
DR RefSeq; WP_011585520.1; NZ_FPJX01000013.1.
DR PDB; 3Q45; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I=1-368.
DR PDB; 3Q4D; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I=1-368.
DR PDBsum; 3Q45; -.
DR PDBsum; 3Q4D; -.
DR AlphaFoldDB; Q11T61; -.
DR SMR; Q11T61; -.
DR STRING; 269798.CHU_2140; -.
DR EnsemblBacteria; ABG59403; ABG59403; CHU_2140.
DR KEGG; chu:CHU_2140; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_0_10; -.
DR OMA; MFGCYSD; -.
DR OrthoDB; 951991at2; -.
DR Proteomes; UP000001822; Chromosome.
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; Reference proteome.
FT CHAIN 1..368
FT /note="D-Ala-D/L-Ala epimerase"
FT /id="PRO_0000429644"
FT BINDING 135
FT /ligand="substrate"
FT BINDING 160..162
FT /ligand="substrate"
FT BINDING 190
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
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 265
FT /ligand="substrate"
FT BINDING 318..320
FT /ligand="substrate"
FT STRAND 2..21
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 24..38
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 59..73
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 81..91
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 96..114
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 118..121
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 141..153
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 167..181
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 183..190
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 197..207
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 208..210
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 212..216
FT /evidence="ECO:0007829|PDB:3Q4D"
FT HELIX 221..226
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 227..232
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 247..255
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:3Q45"
FT TURN 266..270
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 272..284
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 298..308
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 314..317
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 321..324
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 325..327
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 330..333
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 347..350
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:3Q45"
FT TURN 356..358
FT /evidence="ECO:0007829|PDB:3Q45"
FT HELIX 359..361
FT /evidence="ECO:0007829|PDB:3Q45"
FT STRAND 362..367
FT /evidence="ECO:0007829|PDB:3Q45"
SQ SEQUENCE 368 AA; 40311 MW; 1884D7929CF22AB8 CRC64;
MIITQVELYK SPVKLKEPFK ISLGILTHAN NVIVRIHTAS GHIGYGECSP FMTIHGESMD
TAFIVGQYLA KGLIGTSCLD IVSNSLLMDA IIYGNSCIKS AFNIALYDLA AQHAGLPLYA
FLGGKKDKII QTDYTVSIDE PHKMAADAVQ IKKNGFEIIK VKVGGSKELD VERIRMIREA
AGDSITLRID ANQGWSVETA IETLTLLEPY NIQHCEEPVS RNLYTALPKI RQACRIPIMA
DESCCNSFDA ERLIQIQACD SFNLKLSKSA GITNALNIIR LAEQAHMPVQ VGGFLESRLG
FTAAAHVALV SKTICYYDFD TPLMFEADPV RGGIVYQQRG IIEVPETAGL GAGYQKDYLS
GLEKICIN
