PHYDA_ECOLI
ID PHYDA_ECOLI Reviewed; 461 AA.
AC Q46806; Q2M9W7;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2001, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=D-phenylhydantoinase;
DE EC=3.5.2.- {ECO:0000269|PubMed:11092864};
DE AltName: Full=Hydantoin-utilizing enzyme HyuA;
GN Name=hyuA; Synonyms=ygeZ; OrderedLocusNames=b2873, JW2841;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP PROTEIN SEQUENCE OF 1-16, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=11092864; DOI=10.1128/jb.182.24.7021-7028.2000;
RA Kim G.J., Lee D.E., Kim H.-S.;
RT "Functional expression and characterization of the two cyclic
RT amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from
RT Escherichia coli.";
RL J. Bacteriol. 182:7021-7028(2000).
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:0000269|PubMed:11092864}.
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:0000269|PubMed:11092864};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11092864, ECO:0000305};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:11092864, ECO:0000305};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:11092864, ECO:0000305};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11092864, ECO:0000305};
CC Note=Binds 2 divalent metal cations per subunit. Can use zinc, nickel,
CC cobalt or manganese. {ECO:0000269|PubMed:11092864, ECO:0000305};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.8 mM for phenylhydantoin {ECO:0000269|PubMed:11092864};
CC KM=32.8 mM for hydroxyphenylhydantoin {ECO:0000269|PubMed:11092864};
CC KM=138 mM for hydantoin {ECO:0000269|PubMed:11092864};
CC Vmax=12.6 umol/min/mg enzyme with hydroxyphenylhydantoin as substrate
CC {ECO:0000269|PubMed:11092864};
CC Vmax=3.3 umol/min/mg enzyme with phenylhydantoin as substrate
CC {ECO:0000269|PubMed:11092864};
CC Vmax=0.15 umol/min/mg enzyme with hydantoin as substrate
CC {ECO:0000269|PubMed:11092864};
CC Note=Hydantoin derivatives with an aliphatic or no side chain at
CC their 5'-position results in a much lower level of activity than
CC those with aromatic side chains at the 5'-position.;
CC pH dependence:
CC Optimum pH is 8-8.5. {ECO:0000269|PubMed:11092864};
CC Temperature dependence:
CC Optimum temperature is 45-50 degrees Celsius.
CC {ECO:0000269|PubMed:11092864};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:11092864}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two divalent
CC metal cations. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA83054.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U28375; AAA83054.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC75911.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE76939.1; -; Genomic_DNA.
DR PIR; A65071; A65071.
DR RefSeq; NP_417349.4; NC_000913.3.
DR RefSeq; WP_001264442.1; NZ_LN832404.1.
DR AlphaFoldDB; Q46806; -.
DR SMR; Q46806; -.
DR BioGRID; 4261249; 13.
DR IntAct; Q46806; 2.
DR STRING; 511145.b2873; -.
DR PaxDb; Q46806; -.
DR PRIDE; Q46806; -.
DR EnsemblBacteria; AAC75911; AAC75911; b2873.
DR EnsemblBacteria; BAE76939; BAE76939; BAE76939.
DR GeneID; 947359; -.
DR KEGG; ecj:JW2841; -.
DR KEGG; eco:b2873; -.
DR PATRIC; fig|1411691.4.peg.3861; -.
DR EchoBASE; EB2868; -.
DR eggNOG; COG0044; Bacteria.
DR HOGENOM; CLU_015572_2_0_6; -.
DR InParanoid; Q46806; -.
DR OMA; SAETHHM; -.
DR PhylomeDB; Q46806; -.
DR BioCyc; EcoCyc:G7492-MON; -.
DR BioCyc; MetaCyc:G7492-MON; -.
DR SABIO-RK; Q46806; -.
DR PRO; PR:Q46806; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; 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; IDA:EcoliWiki.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
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 1: Evidence at protein level;
KW Direct protein sequencing; Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..461
FT /note="D-phenylhydantoinase"
FT /id="PRO_0000165937"
FT BINDING 59
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 61
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
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:0000250"
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:0000250"
FT BINDING 156
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 182
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 239
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 286
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 151
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 461 AA; 51025 MW; 5525E62DB7F8DB5B CRC64;
MRVLIKNGTV VNADGQAKQD LLIESGIVRQ LGNNISPQLP YEEIDATGCY VFPGGVDVHT
HFNIDVGIAR SCDDFFTGTR AAACGGTTTI IDHMGFGPNG CRLRHQLEVY RGYAAHKAVI
DYSFHGVIQH INHAILDEIP MIVEEGLSSF 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
