HYDA_GEOSE
ID HYDA_GEOSE Reviewed; 471 AA.
AC Q45515;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=D-hydantoinase;
DE EC=3.5.2.-;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, COFACTOR,
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=NS1122A;
RX PubMed=7765480; DOI=10.1271/bbb.58.1621;
RA Mukohara Y., Ishikawa T., Watabe K., Nakamura H.;
RT "A thermostable hydantoinase of Bacillus stearothermophilus NS1122A:
RT cloning, sequencing, and high expression of the enzyme gene, and some
RT properties of the expressed enzyme.";
RL Biosci. Biotechnol. Biochem. 58:1621-1626(1994).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.01 ANGSTROMS) OF 1-459 IN COMPLEX WITH ZINC IONS,
RP SUBUNIT, COFACTOR, AND CARBOXYLATION AT LYS-150.
RX PubMed=12135362; DOI=10.1021/bi0201567;
RA Cheon Y.-H., Kim H.-S., Han K.-H., Abendroth J., Niefind K., Schomburg D.,
RA Wang J., Kim Y.;
RT "Crystal structure of D-hydantoinase from Bacillus stearothermophilus:
RT insight into the stereochemistry of enantioselectivity.";
RL Biochemistry 41:9410-9417(2002).
CC -!- FUNCTION: Catalyzes the stereospecific hydrolysis of the cyclic amide
CC bond of D-hydantoin. Has no activity on dihydropyrimidines.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12135362, ECO:0000269|PubMed:7765480};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:12135362, ECO:0000269|PubMed:7765480};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:12135362, ECO:0000269|PubMed:7765480};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:12135362, ECO:0000269|PubMed:7765480};
CC Note=Binds 2 Zn(2+) ions per subunit. Can also use Ni(2+), Co(2+) or
CC Mn(2+). {ECO:0000269|PubMed:12135362, ECO:0000269|PubMed:7765480};
CC -!- ACTIVITY REGULATION: Completely inhibited by p-chloromercuribenzoate
CC and partially inhibited by metal chelating agents.
CC {ECO:0000269|PubMed:7765480}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC The optimal activity is at pH 8.8 for manganese-containing form and
CC pH 8.5 for cobalt-containing form. The oligomer is thermostable and
CC retains full initial activity at 40-60 degrees Celsius.
CC {ECO:0000269|PubMed:7765480};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12135362}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two zinc ions.
CC {ECO:0000269|PubMed:12135362}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {ECO:0000305}.
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DR EMBL; S73773; AAC60487.1; -; Genomic_DNA.
DR PIR; JC2310; JC2310.
DR PDB; 1K1D; X-ray; 3.01 A; A/B/C/D/E/F/G/H=1-459.
DR PDBsum; 1K1D; -.
DR AlphaFoldDB; Q45515; -.
DR SMR; Q45515; -.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR BRENDA; 3.5.2.2; 623.
DR EvolutionaryTrace; Q45515; -.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd01314; D-HYD; 1.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
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; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR02033; D-hydantoinase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Metal-binding; Zinc.
FT CHAIN 1..471
FT /note="D-hydantoinase"
FT /id="PRO_0000165933"
FT BINDING 58
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 60
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 155
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 183
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 239
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 288
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 315
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12135362,
FT ECO:0007744|PDB:1K1D"
FT BINDING 337
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT MOD_RES 150
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:12135362"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 16..23
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 25..34
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 74..83
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 86..93
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 101..112
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 113..115
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 117..125
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 131..142
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 156..159
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 163..176
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 206..210
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 214..231
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 234..237
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 243..254
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 258..263
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 265..269
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 281..285
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 296..306
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 307..309
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 321..324
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 332..334
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 342..344
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 345..352
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 361..368
FT /evidence="ECO:0007829|PDB:1K1D"
FT HELIX 370..375
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 379..381
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 393..403
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 406..408
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 411..414
FT /evidence="ECO:0007829|PDB:1K1D"
FT TURN 417..420
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 422..432
FT /evidence="ECO:0007829|PDB:1K1D"
FT STRAND 435..439
FT /evidence="ECO:0007829|PDB:1K1D"
SQ SEQUENCE 471 AA; 51725 MW; FB75A507727292FB CRC64;
MTKLIKNGTI VTATDIYEAD LLIQDGKIAV IGRNLDESGA EVIDATGCYV FPGGIDPHTH
LDMPFGGTVT KDDFESGTIA AAFGGTTTII DFCLTNKGEP LKKAIETWHN KATGKAVIDY
GFHLMISEIT DDVLEELPKV IEEEGITSFK VFMAYKDVFQ ADDGTLYRTL VAAKELGALV
MVHAENGDVI DYLTKKALED GHTDPIYHAL TRPPELEGEA TGRACQLTEL AGSQLYVVHV
SCAQAVEKIA EARNKGLNVW GETCPQYLVL DQSYLEKPNF EGAKYVWSPP LREKWHQEVL
WNALKNGQLQ TLGSDQCSFD FKGQKELGRG DFTKIPNGGP IIEDRVSILF SEGVKKGRIT
LNQFVDIVST RIAKLFGLFP KKGTIAVGAD ADLVIFDPTV ERVISAETHH MAVDYNPFEG
MKVTGEPVSV LCRGEFVVRD KQFVGKPGYG QYVKRAKYGA LMADQDVVKM S
