PHYDA_SHIBS
ID PHYDA_SHIBS Reviewed; 461 AA.
AC Q31WE3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-FEB-2008, sequence version 2.
DT 03-AUG-2022, entry version 93.
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}; OrderedLocusNames=SBO_3111;
OS Shigella boydii serotype 4 (strain Sb227).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=300268;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sb227;
RX PubMed=16275786; DOI=10.1093/nar/gki954;
RA Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J.,
RA Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J.,
RA Xu J., Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J.,
RA Jin Q.;
RT "Genome dynamics and diversity of Shigella species, the etiologic agents of
RT bacillary dysentery.";
RL Nucleic Acids Res. 33:6445-6458(2005).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABB67615.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000036; ABB67615.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_001264452.1; NC_007613.1.
DR AlphaFoldDB; Q31WE3; -.
DR SMR; Q31WE3; -.
DR EnsemblBacteria; ABB67615; ABB67615; SBO_3111.
DR GeneID; 58463780; -.
DR KEGG; sbo:SBO_3111; -.
DR HOGENOM; CLU_015572_2_0_6; -.
DR Proteomes; UP000007067; 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_0000317656"
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; 51043 MW; E08827820DECD88D 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 NVREQDKLWC
GISDGAIDVV ATDHCTFSMA QRLQISKGDF SRCPNGLPGV ENRMQLLFSS GVMTGRITPE
RFVELTSAMP ARLFGLWPQK GLLAPGSDGD VVIIDPRQSQ QIQHRHLHDN ADYSPWEGFT
CQGAIVRTLS RGETIFCDGT FTGKAGRGRF LRRKPFVPPV L
