ID AREP_HERA2 Reviewed; 356 AA.
AC A9B055;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 27-MAR-2024, entry version 87.
DE RecName: Full=Aromatic dipeptide epimerase;
DE EC=5.1.1.-;
GN OrderedLocusNames=Haur_1114;
OS Herpetosiphon aurantiacus (strain ATCC 23779 / DSM 785 / 114-95).
OC Bacteria; Chloroflexota; Chloroflexia; Herpetosiphonales;
OC Herpetosiphonaceae; Herpetosiphon.
OX NCBI_TaxID=316274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 23779 / DSM 785 / 114-95;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Kiss H., Brettin T., Bruce D., Detter J.C., Han C.,
RA Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E.,
RA Bryant D.A., Richardson P.;
RT "Complete sequence of chromosome of Herpetosiphon aurantiacus ATCC 23779.";
RL Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-355, FUNCTION, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 23779 / DSM 785 / 114-95;
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: Has epimerase activity with a variety of hydrophobic
CC dipeptides (in vitro). Enzyme activity is highest with L-Phe-L-Tyr, but
CC is still relatively low, suggesting that L-Phe-L-Tyr is not the
CC physiological substrate. {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=4.8 mM for L-Phe-L-Tyr {ECO:0000269|PubMed:22392983};
CC Note=kcat is 4.7 sec(-1) for epimerization of L-Phe-L-Tyr.;
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; CP000875; ABX03762.1; -; Genomic_DNA.
DR PDB; 3IK4; X-ray; 2.10 A; A/B/C/D=2-355.
DR PDBsum; 3IK4; -.
DR AlphaFoldDB; A9B055; -.
DR SMR; A9B055; -.
DR STRING; 316274.Haur_1114; -.
DR KEGG; hau:Haur_1114; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_1_0; -.
DR InParanoid; A9B055; -.
DR BioCyc; HAUR316274:GHYA-1135-MONOMER; -.
DR EvolutionaryTrace; A9B055; -.
DR Proteomes; UP000000787; 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; Enolase-like C-terminal domain; 1.
DR Gene3D; 3.30.390.10; Enolase-like, N-terminal domain; 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 PANTHER; PTHR48073:SF2; O-SUCCINYLBENZOATE SYNTHASE; 1.
DR PANTHER; PTHR48073; O-SUCCINYLBENZOATE SYNTHASE-RELATED; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDG00180; muconate_cycloisomerase; 1.
DR SFLD; SFLDF00009; o-succinylbenzoate_synthase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; Enolase C-terminal domain-like; 1.
DR SUPFAM; SSF54826; Enolase N-terminal domain-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Metal-binding.
FT CHAIN 1..356
FT /note="Aromatic dipeptide epimerase"
FT /id="PRO_0000429648"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 161..163
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305"
FT BINDING 244
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305"
FT BINDING 268
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 320..322
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT STRAND 4..18
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 21..23
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 30..40
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:3IK4"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 61..71
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:3IK4"
FT TURN 75..77
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 83..93
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 98..115
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 142..154
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 169..182
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 274..287
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 290..293
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 300..313
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:3IK4"
FT HELIX 323..326
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 331..335
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:3IK4"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:3IK4"
SQ SEQUENCE 356 AA; 36784 MW; E9E71AE046B97188 CRC64;
MPTTIQAISA EAINLPLTEP FAIASGAQAV AANVLVKVQL ADGTLGLGEA APFPAVSGET
QTGTSAAIER LQSHLLGADV RGWRKLAAML DHAEHEAAAA RCGLEMAMLD ALTRHYHMPL
HVFFGGVSKQ LETDMTITAG DEVHAAASAK AILARGIKSI KVKTAGVDVA YDLARLRAIH
QAAPTAPLIV DGNCGYDVER ALAFCAACKA ESIPMVLFEQ PLPREDWAGM AQVTAQSGFA
VAADESARSA HDVLRIAREG TASVINIKLM KAGVAEGLKM IAIAQAAGLG LMIGGMVESI
LAMSFSANLA AGNGGFDFID LDTPLFIAEH PFIGGFAQTG GTLQLADVAG HGVNLA
//
