HYDA_RALPI
ID HYDA_RALPI Reviewed; 457 AA.
AC Q8VTT5;
DT 06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=D-hydantoinase;
DE EC=3.5.2.-;
GN Name=hyuA;
OS Ralstonia pickettii (Burkholderia pickettii).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Ralstonia.
OX NCBI_TaxID=329;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Xu Z., Jiang W.-H., Yang Y.-L.;
RT "Cloning, sequencing and expression of a hydantoinase gene of Burholderia
RT pickettii.";
RL Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH ZINC IONS, SUBUNIT,
RP CARBOXYLATION AT LYS-148, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=12837777; DOI=10.1128/jb.185.14.4038-4049.2003;
RA Xu Z., Liu Y., Yang Y., Jiang W., Arnold E., Ding J.;
RT "Crystal structure of D-hydantoinase from Burkholderia pickettii at a
RT resolution of 2.7 Angstroms: insights into the molecular basis of enzyme
RT thermostability.";
RL J. Bacteriol. 185:4038-4049(2003).
CC -!- FUNCTION: Catalyzes the stereospecific hydrolysis of the cyclic amide
CC bond of D-hydantoin derivatives. {ECO:0000250}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12837777};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000269|PubMed:12837777};
CC -!- SUBUNIT: Homodimer and homotetramer. {ECO:0000269|PubMed:12837777}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two zinc ions.
CC {ECO:0000269|PubMed:12837777}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {ECO:0000305}.
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DR EMBL; AF320814; AAL37185.1; -; Genomic_DNA.
DR PDB; 1NFG; X-ray; 2.70 A; A/B/C/D=1-457.
DR PDBsum; 1NFG; -.
DR AlphaFoldDB; Q8VTT5; -.
DR SMR; Q8VTT5; -.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR BRENDA; 3.5.2.2; 5160.
DR EvolutionaryTrace; Q8VTT5; -.
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 InterPro; IPR011612; Urease_alpha_N_dom.
DR Pfam; PF01979; Amidohydro_1; 1.
DR Pfam; PF00449; Urease_alpha; 1.
DR SUPFAM; SSF51338; SSF51338; 2.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR02033; D-hydantoinase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Phosphoprotein; Zinc.
FT CHAIN 1..457
FT /note="D-hydantoinase"
FT /id="PRO_0000165934"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 59
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 148
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 148
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 153
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 181
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 237
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 286
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT MOD_RES 69
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q14117"
FT MOD_RES 148
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:12837777,
FT ECO:0007744|PDB:1NFG"
FT STRAND 3..12
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 15..24
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 73..82
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 85..93
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 116..124
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 130..135
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 139..142
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 146..153
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 154..157
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 161..174
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 185..197
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 204..208
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 212..229
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 241..253
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 270..274
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 276..278
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 279..283
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 292..303
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 319..328
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 340..342
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 343..352
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 358..365
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 367..372
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 376..378
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 379..381
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 390..400
FT /evidence="ECO:0007829|PDB:1NFG"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:1NFG"
FT TURN 414..417
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 419..429
FT /evidence="ECO:0007829|PDB:1NFG"
FT STRAND 432..436
FT /evidence="ECO:0007829|PDB:1NFG"
SQ SEQUENCE 457 AA; 49932 MW; 1DC2301D2A9E276E CRC64;
MDIIIKNGTI VTADGISRAD LGIKDGKITQ IGGALGPAER TIDAAGRYVF PGGIDVHTHV
ETVSFNTQSA DTFATATVAA ACGGTTTIVD FCQQDRGHSL AEAVAKWDGM AGGKSAIDYG
YHIIVLDPTD SVIEELEVLP DLGITSFKVF MAYRGMNMID DVTLLKTLDK AVKTGSLVMV
HAENGDAADY LRDKFVAEGK TAPIYHALSR PPRVEAEATA RALALAEIVN APIYIVHVTC
EESLEEVMRA KSRGVRALAE TCTHYLYLTK EDLERPDFEG AKYVFTPPAR AKKDHDVLWN
ALRNGVFETV SSDHCSWLFK GHKDRGRNDF RAIPNGAPGV EERLMMVYQG VNEGRISLTQ
FVELVATRPA KVFGMFPQKG TIAVGSDADI VLWDPEAEMV IEQTAMHNAM DYSSYEGHKV
KGVPKTVLLR GKVIVDEGSY VGEPTDGKFL KRRKYKQ
