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Protein

D-hydantoinase

Gene
N/A
Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.

Cofactori

Zn2+2 Publications, Ni2+2 Publications, Co2+2 Publications, Mn2+2 PublicationsNote: Binds 2 Zn2+ ions per subunit. Can also use Ni2+, Co2+ or Mn2+.2 Publications

Enzyme regulationi

Completely inhibited by p-chloromercuribenzoate and partially inhibited by metal chelating agents.1 Publication

Temperature dependencei

The optimal activity is at pH 8.8 for manganese-containing form and pH 8.5 for cobalt-containing form. The oligomer is thermostable and retains full initial activity at 40-60 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi58 – 581Zinc 1Combined sources1 Publication
Metal bindingi60 – 601Zinc 1Combined sources1 Publication
Metal bindingi150 – 1501Zinc 1; via carbamate groupCombined sources1 Publication
Metal bindingi150 – 1501Zinc 2; via carbamate groupCombined sources1 Publication
Binding sitei155 – 1551SubstrateBy similarity
Metal bindingi183 – 1831Zinc 2Combined sources1 Publication
Metal bindingi239 – 2391Zinc 2Combined sources1 Publication
Binding sitei288 – 2881Substrate; via amide nitrogen and carbonyl oxygenBy similarity
Metal bindingi315 – 3151Zinc 1Combined sources1 Publication
Binding sitei337 – 3371Substrate; via carbonyl oxygenBy similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.2.2. 623.

Names & Taxonomyi

Protein namesi
Recommended name:
D-hydantoinase (EC:3.5.2.-)
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 471471D-hydantoinasePRO_0000165933Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei150 – 1501N6-carboxylysine1 Publication

Post-translational modificationi

Carbamylation allows a single lysine to coordinate two zinc ions.1 Publication

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

1
471
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Beta strandi16 – 238Combined sources
Beta strandi25 – 3410Combined sources
Beta strandi49 – 524Combined sources
Beta strandi54 – 596Combined sources
Beta strandi66 – 683Combined sources
Helixi74 – 8310Combined sources
Beta strandi86 – 938Combined sources
Helixi101 – 11212Combined sources
Turni113 – 1153Combined sources
Beta strandi117 – 1259Combined sources
Helixi131 – 14212Combined sources
Beta strandi148 – 1558Combined sources
Turni156 – 1594Combined sources
Helixi163 – 17614Combined sources
Beta strandi179 – 1835Combined sources
Helixi187 – 19913Combined sources
Helixi206 – 2105Combined sources
Helixi214 – 23118Combined sources
Beta strandi234 – 2374Combined sources
Helixi243 – 25412Combined sources
Beta strandi258 – 2636Combined sources
Helixi265 – 2695Combined sources
Helixi272 – 2754Combined sources
Helixi281 – 2855Combined sources
Helixi296 – 30611Combined sources
Beta strandi307 – 3093Combined sources
Turni321 – 3244Combined sources
Helixi325 – 3284Combined sources
Helixi332 – 3343Combined sources
Turni342 – 3443Combined sources
Helixi345 – 3528Combined sources
Helixi354 – 3563Combined sources
Helixi361 – 3688Combined sources
Helixi370 – 3756Combined sources
Turni379 – 3813Combined sources
Beta strandi393 – 40311Combined sources
Turni406 – 4083Combined sources
Beta strandi411 – 4144Combined sources
Turni417 – 4204Combined sources
Beta strandi422 – 43211Combined sources
Beta strandi435 – 4395Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K1DX-ray3.01A/B/C/D/E/F/G/H1-459[»]
ProteinModelPortaliQ45515.
SMRiQ45515. Positions 1-459.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ45515.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro-rel.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
IPR032466. Metal_Hydrolase.
[Graphical view]
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
SSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.

Sequencei

Sequence statusi: Complete.

Q45515-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKLIKNGTI VTATDIYEAD LLIQDGKIAV IGRNLDESGA EVIDATGCYV
60 70 80 90 100
FPGGIDPHTH LDMPFGGTVT KDDFESGTIA AAFGGTTTII DFCLTNKGEP
110 120 130 140 150
LKKAIETWHN KATGKAVIDY GFHLMISEIT DDVLEELPKV IEEEGITSFK
160 170 180 190 200
VFMAYKDVFQ ADDGTLYRTL VAAKELGALV MVHAENGDVI DYLTKKALED
210 220 230 240 250
GHTDPIYHAL TRPPELEGEA TGRACQLTEL AGSQLYVVHV SCAQAVEKIA
260 270 280 290 300
EARNKGLNVW GETCPQYLVL DQSYLEKPNF EGAKYVWSPP LREKWHQEVL
310 320 330 340 350
WNALKNGQLQ TLGSDQCSFD FKGQKELGRG DFTKIPNGGP IIEDRVSILF
360 370 380 390 400
SEGVKKGRIT LNQFVDIVST RIAKLFGLFP KKGTIAVGAD ADLVIFDPTV
410 420 430 440 450
ERVISAETHH MAVDYNPFEG MKVTGEPVSV LCRGEFVVRD KQFVGKPGYG
460 470
QYVKRAKYGA LMADQDVVKM S
Length:471
Mass (Da):51,725
Last modified:November 1, 1996 - v1
Checksum:iFB75A507727292FB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S73773 Genomic DNA. Translation: AAC60487.1.
PIRiJC2310.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S73773 Genomic DNA. Translation: AAC60487.1.
PIRiJC2310.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K1DX-ray3.01A/B/C/D/E/F/G/H1-459[»]
ProteinModelPortaliQ45515.
SMRiQ45515. Positions 1-459.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.5.2.2. 623.

Miscellaneous databases

EvolutionaryTraceiQ45515.

Family and domain databases

Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro-rel.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
IPR032466. Metal_Hydrolase.
[Graphical view]
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
SSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "A thermostable hydantoinase of Bacillus stearothermophilus NS1122A: cloning, sequencing, and high expression of the enzyme gene, and some properties of the expressed enzyme."
    Mukohara Y., Ishikawa T., Watabe K., Nakamura H.
    Biosci. Biotechnol. Biochem. 58:1621-1626(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: NS1122A.
  2. "Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity."
    Cheon Y.-H., Kim H.-S., Han K.-H., Abendroth J., Niefind K., Schomburg D., Wang J., Kim Y.
    Biochemistry 41:9410-9417(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.01 ANGSTROMS) OF 1-459 IN COMPLEX WITH ZINC IONS, SUBUNIT, COFACTOR, CARBAMYLATION AT LYS-150.

Entry informationi

Entry nameiHYDA_GEOSE
AccessioniPrimary (citable) accession number: Q45515
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: January 20, 2016
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.