PHYDA_ECO55
ID PHYDA_ECO55 Reviewed; 461 AA.
AC B7LF59;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=D-phenylhydantoinase {ECO:0000255|HAMAP-Rule:MF_01644};
DE EC=3.5.2.- {ECO:0000255|HAMAP-Rule:MF_01644};
DE AltName: Full=Hydantoin-utilizing enzyme HyuA {ECO:0000255|HAMAP-Rule:MF_01644};
GN Name=hyuA {ECO:0000255|HAMAP-Rule:MF_01644};
GN OrderedLocusNames=EC55989_3160;
OS Escherichia coli (strain 55989 / EAEC).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=585055;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=55989 / EAEC;
RX PubMed=19165319; DOI=10.1371/journal.pgen.1000344;
RA Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P.,
RA Bingen E., Bonacorsi S., Bouchier C., Bouvet O., Calteau A., Chiapello H.,
RA Clermont O., Cruveiller S., Danchin A., Diard M., Dossat C., Karoui M.E.,
RA Frapy E., Garry L., Ghigo J.M., Gilles A.M., Johnson J., Le Bouguenec C.,
RA Lescat M., Mangenot S., Martinez-Jehanne V., Matic I., Nassif X., Oztas S.,
RA Petit M.A., Pichon C., Rouy Z., Ruf C.S., Schneider D., Tourret J.,
RA Vacherie B., Vallenet D., Medigue C., Rocha E.P.C., Denamur E.;
RT "Organised genome dynamics in the Escherichia coli species results in
RT highly diverse adaptive paths.";
RL PLoS Genet. 5:E1000344-E1000344(2009).
CC -!- FUNCTION: Catalyzes the stereospecific hydrolysis of the cyclic amide
CC bond of D-hydantoin derivatives with an aromatic side chains at the 5'-
CC position. Has no activity on dihydropyrimidines. The physiological
CC function is unknown. {ECO:0000255|HAMAP-Rule:MF_01644}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-5-phenylhydantoin + H2O = H(+) + N-carbamoyl-D-
CC phenylglycine; Xref=Rhea:RHEA:51664, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:140750, ChEBI:CHEBI:140758;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01644};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01644};
CC Note=Binds 2 divalent metal cations per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_01644};
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01644}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two divalent
CC metal cations. {ECO:0000255|HAMAP-Rule:MF_01644}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {ECO:0000255|HAMAP-
CC Rule:MF_01644}.
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DR EMBL; CU928145; CAU99105.1; -; Genomic_DNA.
DR RefSeq; WP_001264447.1; NC_011748.1.
DR AlphaFoldDB; B7LF59; -.
DR SMR; B7LF59; -.
DR EnsemblBacteria; CAU99105; CAU99105; EC55989_3160.
DR KEGG; eck:EC55989_3160; -.
DR HOGENOM; CLU_015572_2_0_6; -.
DR OMA; SAETHHM; -.
DR Proteomes; UP000000746; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0016812; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IEA:InterPro.
DR CDD; cd01314; D-HYD; 1.
DR Gene3D; 2.30.40.10; -; 1.
DR HAMAP; MF_01644; D_hydantoinase; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR023766; D_phenylhydantoinase.
DR InterPro; IPR011778; Hydantoinase/dihydroPyrase.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR Pfam; PF01979; Amidohydro_1; 1.
DR SUPFAM; SSF51338; SSF51338; 2.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR02033; D-hydantoinase; 1.
PE 3: Inferred from homology;
KW Hydrolase; Metal-binding.
FT CHAIN 1..461
FT /note="D-phenylhydantoinase"
FT /id="PRO_1000186909"
FT BINDING 59
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 61
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 151
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 151
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 156
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 182
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 239
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 286
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 313
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
FT MOD_RES 151
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01644"
SQ SEQUENCE 461 AA; 51057 MW; DBEBA584179E4B94 CRC64;
MRVLIKNGTV VNADGQAKQD LLIESGIVRQ LGNNISPQLP YEEIDATGCY VFPGGVDVHT
HFNIDVGIAR SCDDFFTGTR AAACGGTTTI IDHMGFGPNG CRLRHQLEVY RGYAAHKAVI
DYSFHGVIQH INHAILDEIP MMVEEGLSSF KLYLTYQYKL NDDEVLQALR RLHESGALTT
VHPENDAAIA SKRAEFIAAG LTAPRYHALS RPLECEAEAI ARMINLAQIA GNAPLYIVHL
SNGLGLDYLR LARANHQPVW VETCPQYLLL DERSYDTEDG MKFILSPPLR NIREQDKLWC
GISDGAIDVV ATDHCTFSMA QRLQISKGDF SRCPNGLPGV ENRMQLLFSS GVMTGRITPE
RFVELTSAMP ARLFGLWPQK GLLAPGSDGD VVIIDPRQSQ QIQHRHLHDN ADYSPWEGFT
CQGAIVRTLS RGETIFCDGT FTGKAGRGRF LRRKPFVPPV L
