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P69996

- URE1_HELPY

UniProt

P69996 - URE1_HELPY

Protein

Urease subunit beta

Gene

ureB

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 82 (01 Oct 2014)
      Sequence version 1 (04 Jan 2005)
      Previous versions | rss
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    Functioni

    Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach.1 Publication

    Catalytic activityi

    Urea + H2O = CO2 + 2 NH3.3 PublicationsUniRule annotation

    Cofactori

    Binds 2 nickel ions per subunit.

    Kineticsi

    1. KM=0.48 mM for urea2 Publications

    Vmax=1.1 mmol/min/mg enzyme2 Publications

    pH dependencei

    Optimum pH is 8.0. Active from pH 4.0 to 10.0. In unbuffered solutions, the dodecameric complex is active at pH3.0.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi136 – 1361Nickel 1; via tele nitrogen
    Metal bindingi138 – 1381Nickel 1; via tele nitrogen
    Metal bindingi219 – 2191Nickel 1; via carbamate group
    Metal bindingi219 – 2191Nickel 2; via carbamate group
    Binding sitei221 – 2211SubstrateCurated
    Metal bindingi248 – 2481Nickel 2; via pros nitrogen
    Metal bindingi274 – 2741Nickel 2; via tele nitrogen
    Active sitei322 – 3221Proton donorCurated
    Metal bindingi362 – 3621Nickel 1

    GO - Molecular functioni

    1. nickel cation binding Source: UniProtKB-HAMAP
    2. urease activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. pathogenesis Source: UniProtKB-KW
    2. urea catabolic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Virulence

    Keywords - Ligandi

    Metal-binding, Nickel

    Enzyme and pathway databases

    BioCyciHPY:HP0072-MONOMER.
    UniPathwayiUPA00258; UER00370.

    Protein family/group databases

    MEROPSiM38.982.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Urease subunit betaUniRule annotation (EC:3.5.1.5UniRule annotation)
    Alternative name(s):
    Urea amidohydrolase subunit betaUniRule annotation
    Gene namesi
    Name:ureBUniRule annotation
    Synonyms:hpuB
    Ordered Locus Names:HP_0072
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    ProteomesiUP000000429: Chromosome

    Subcellular locationi

    Cytoplasm 1 PublicationUniRule annotation
    Note: Also associates with the outer membrane upon autolysis of neighboring bacteria.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells do not express urease.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 569569Urease subunit betaPRO_0000067533Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei219 – 2191N6-carboxylysine1 PublicationUniRule annotation

    Post-translational modificationi

    Carbamylation allows a single lysine to coordinate two nickel ions.1 PublicationUniRule annotation

    Proteomic databases

    PRIDEiP69996.

    Expressioni

    Inductioni

    By nickel ions.2 Publications

    Interactioni

    Subunit structurei

    Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits. Four heterohexamers assemble to form a 16 nm dodecameric complex.1 PublicationUniRule annotation

    Protein-protein interaction databases

    IntActiP69996. 12 interactions.
    MINTiMINT-1567059.
    STRINGi85962.HP0072.

    Structurei

    Secondary structure

    1
    569
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 53
    Helixi6 – 105
    Beta strandi20 – 223
    Beta strandi29 – 313
    Beta strandi49 – 535
    Turni54 – 563
    Beta strandi67 – 7711
    Beta strandi80 – 8910
    Beta strandi92 – 976
    Turni102 – 1043
    Beta strandi105 – 1073
    Helixi110 – 1123
    Beta strandi119 – 1224
    Beta strandi127 – 1304
    Beta strandi132 – 1387
    Helixi144 – 1507
    Beta strandi153 – 1597
    Helixi165 – 1695
    Helixi175 – 18612
    Beta strandi189 – 19810
    Helixi204 – 2129
    Beta strandi216 – 2205
    Helixi222 – 2243
    Helixi228 – 24013
    Beta strandi244 – 2474
    Helixi258 – 2658
    Beta strandi270 – 2723
    Turni273 – 2764
    Turni283 – 2853
    Helixi286 – 2916
    Beta strandi295 – 2995
    Helixi301 – 3033
    Helixi310 – 32011
    Turni321 – 3233
    Helixi329 – 33810
    Helixi341 – 35212
    Beta strandi365 – 3673
    Helixi372 – 38716
    Beta strandi395 – 3973
    Helixi399 – 4068
    Helixi407 – 4093
    Helixi411 – 4166
    Turni420 – 4223
    Beta strandi423 – 4264
    Beta strandi434 – 4374
    Turni439 – 4446
    Beta strandi447 – 4515
    Beta strandi454 – 4607
    Beta strandi465 – 4684
    Beta strandi470 – 4723
    Beta strandi474 – 4774
    Helixi479 – 4813
    Helixi485 – 4895
    Beta strandi491 – 4944
    Helixi496 – 5005
    Helixi503 – 5064
    Beta strandi511 – 5155
    Helixi524 – 5263
    Beta strandi527 – 5293
    Beta strandi536 – 5383
    Turni540 – 5423
    Beta strandi545 – 5473
    Beta strandi561 – 5633
    Turni564 – 5663

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E9YX-ray3.00B1-569[»]
    1E9ZX-ray3.00B1-569[»]
    ProteinModelPortaliP69996.
    SMRiP69996. Positions 1-569.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP69996.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini131 – 569439UreaseUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the urease family.UniRule annotation
    Contains 1 urease domain.UniRule annotation

    Phylogenomic databases

    KOiK01428.
    OMAiMGQSQAT.
    OrthoDBiEOG6ND0GM.

    Family and domain databases

    Gene3Di2.30.40.10. 1 hit.
    HAMAPiMF_01953. Urease_alpha.
    InterProiIPR006680. Amidohydro_1.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR011612. Urease_alpha_N_dom.
    IPR017950. Urease_AS.
    IPR005848. Urease_asu.
    IPR017951. Urease_asu_c.
    [Graphical view]
    PfamiPF01979. Amidohydro_1. 1 hit.
    PF00449. Urease_alpha. 1 hit.
    [Graphical view]
    PRINTSiPR01752. UREASE.
    SUPFAMiSSF51338. SSF51338. 2 hits.
    TIGRFAMsiTIGR01792. urease_alph. 1 hit.
    PROSITEiPS01120. UREASE_1. 1 hit.
    PS00145. UREASE_2. 1 hit.
    PS51368. UREASE_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P69996-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT    50
    LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIKD GKIAGIGKGG 100
    NKDMQDGVKN NLSVGPATEA LAGEGLIVTA GGIDTHIHFI SPQQIPTAFA 150
    SGVTTMIGGG TGPADGTNAT TITPGRRNLK WMLRAAEEYS MNLGFLAKGN 200
    ASNDASLADQ IEAGAIGFKI HEDWGTTPSA INHALDVADK YDVQVAIHTD 250
    TLNEAGCVED TMAAIAGRTM HTFHTEGAGG GHAPDIIKVA GEHNILPAST 300
    NPTIPFTVNT EAEHMDMLMV CHHLDKSIKE DVQFADSRIR PQTIAAEDTL 350
    HDMGIFSITS SDSQAMGRVG EVITRTWQTA DKNKKEFGRL KEEKGDNDNF 400
    RIKRYLSKYT INPAIAHGIS EYVGSVEVGK VADLVLWSPA FFGVKPNMII 450
    KGGFIALSQM GDANASIPTP QPVYYREMFA HHGKAKYDAN ITFVSQAAYD 500
    KGIKEELGLE RQVLPVKNCR NITKKDMQFN DTTAHIEVNP ETYHVFVDGK 550
    EVTSKPANKV SLAQLFSIF 569
    Length:569
    Mass (Da):61,684
    Last modified:January 4, 2005 - v1
    Checksum:i4C8A6BC6C8295584
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti10 – 101V → A in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti19 – 191D → A(PubMed:2326167)Curated
    Sequence conflicti22 – 221R → C AA sequence (PubMed:1857197)Curated
    Sequence conflicti27 – 271D → C AA sequence (PubMed:1857197)Curated
    Sequence conflicti104 – 1041M → T in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti181 – 1811W → F in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti193 – 1931L → F in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti218 – 2181F → L in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti273 – 2731F → Y in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti540 – 5401P → S in CAA34933. (PubMed:2326167)Curated
    Sequence conflicti554 – 56916SKPAN…LFSIF → LNQPIK in CAA34933. (PubMed:2326167)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60398 Genomic DNA. Translation: AAA25021.1.
    X17079 Genomic DNA. Translation: CAA34933.1.
    AE000511 Genomic DNA. Translation: AAD07143.1.
    M84338 Genomic DNA. No translation available.
    PIRiB38537. URKCBP.
    RefSeqiNP_206872.1. NC_000915.1.
    WP_000724295.1. NC_018939.1.
    YP_006933994.1. NC_018939.1.

    Genome annotation databases

    EnsemblBacteriaiAAD07143; AAD07143; HP_0072.
    GeneIDi13869248.
    899104.
    KEGGiheo:C694_00350.
    hpy:HP0072.
    PATRICi20591347. VBIHelPyl33062_0075.

    Cross-referencesi

    Web resourcesi

    Protein Spotlight

    Going unnoticed - Issue 95 of June 2008

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60398 Genomic DNA. Translation: AAA25021.1 .
    X17079 Genomic DNA. Translation: CAA34933.1 .
    AE000511 Genomic DNA. Translation: AAD07143.1 .
    M84338 Genomic DNA. No translation available.
    PIRi B38537. URKCBP.
    RefSeqi NP_206872.1. NC_000915.1.
    WP_000724295.1. NC_018939.1.
    YP_006933994.1. NC_018939.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1E9Y X-ray 3.00 B 1-569 [» ]
    1E9Z X-ray 3.00 B 1-569 [» ]
    ProteinModelPortali P69996.
    SMRi P69996. Positions 1-569.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P69996. 12 interactions.
    MINTi MINT-1567059.
    STRINGi 85962.HP0072.

    Protein family/group databases

    MEROPSi M38.982.

    Proteomic databases

    PRIDEi P69996.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD07143 ; AAD07143 ; HP_0072 .
    GeneIDi 13869248.
    899104.
    KEGGi heo:C694_00350.
    hpy:HP0072.
    PATRICi 20591347. VBIHelPyl33062_0075.

    Phylogenomic databases

    KOi K01428.
    OMAi MGQSQAT.
    OrthoDBi EOG6ND0GM.

    Enzyme and pathway databases

    UniPathwayi UPA00258 ; UER00370 .
    BioCyci HPY:HP0072-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P69996.

    Family and domain databases

    Gene3Di 2.30.40.10. 1 hit.
    HAMAPi MF_01953. Urease_alpha.
    InterProi IPR006680. Amidohydro_1.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR011612. Urease_alpha_N_dom.
    IPR017950. Urease_AS.
    IPR005848. Urease_asu.
    IPR017951. Urease_asu_c.
    [Graphical view ]
    Pfami PF01979. Amidohydro_1. 1 hit.
    PF00449. Urease_alpha. 1 hit.
    [Graphical view ]
    PRINTSi PR01752. UREASE.
    SUPFAMi SSF51338. SSF51338. 2 hits.
    TIGRFAMsi TIGR01792. urease_alph. 1 hit.
    PROSITEi PS01120. UREASE_1. 1 hit.
    PS00145. UREASE_2. 1 hit.
    PS51368. UREASE_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Shuttle cloning and nucleotide sequences of Helicobacter pylori genes responsible for urease activity."
      Labigne A., Cussac V., Courcoux P.
      J. Bacteriol. 173:1920-1931(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 85P.
    2. "Nucleotide sequence of two genes from Helicobacter pylori encoding for urease subunits."
      Clayton C.L., Pallen M.J., Kleanthous H., Wren B.W., Tabaqchali S.
      Nucleic Acids Res. 18:362-362(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: CPM630.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700392 / 26695.
    4. "Characterization of the Helicobacter pylori urease and purification of its subunits."
      Evans D.J. Jr., Evans D.G., Kirkpatrick S.S., Graham D.Y.
      Microb. Pathog. 10:15-26(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-30, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
    5. "Purification and characterization of urease from Helicobacter pylori."
      Dunn B.E., Campbell G.P., Perez-Perez G.I., Blaser M.J.
      J. Biol. Chem. 265:9464-9469(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-20, CATALYTIC ACTIVITY, KINETIC PARAMETERS, INTERACTION WITH UREA.
    6. "Purification and N-terminal analysis of urease from Helicobacter pylori."
      Hu L.-T., Mobley H.L.T.
      Infect. Immun. 58:992-998(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15.
    7. "Purification and characterization of the urease enzymes of Helicobacter species from humans and animals."
      Turbett G.R., Hoej P.B., Horne R., Mee B.J.
      Infect. Immun. 60:5259-5266(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-12.
      Strain: ATCC 43504 / NCTC 11637 / JCM 7653 / RPH 13487.
    8. "Expression of Helicobacter pylori urease genes in Escherichia coli grown under nitrogen-limiting conditions."
      Cussac V., Ferrero R.L., Labigne A.
      J. Bacteriol. 174:2466-2473(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 565-569, DISRUPTION PHENOTYPE.
      Strain: 85P.
    9. "Purification of recombinant Helicobacter pylori urease apoenzyme encoded by ureA and ureB."
      Hu L.-T., Foxall P.A., Russell R., Mobley H.L.T.
      Infect. Immun. 60:2657-2666(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY.
    10. "A urease-negative mutant of Helicobacter pylori constructed by allelic exchange mutagenesis lacks the ability to colonize the nude mouse stomach."
      Tsuda M., Karita M., Morshed M.G., Okita K., Nakazawa T.
      Infect. Immun. 62:3586-3589(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ROLE IN VIRULENCE.
    11. "Surface localization of Helicobacter pylori urease and a heat shock protein homolog requires bacterial autolysis."
      Phadnis S.H., Parlow M.H., Levy M., Ilver D., Caulkins C.M., Connors J.B., Dunn B.E.
      Infect. Immun. 64:905-912(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    12. "Nickel-responsive induction of urease expression in Helicobacter pylori is mediated at the transcriptional level."
      van Vliet A.H.M., Kuipers E.J., Waidner B., Davies B.J., de Vries N., Penn C.W., Vandenbroucke-Grauls C.M.J.E., Kist M., Bereswill S., Kusters J.G.
      Infect. Immun. 69:4891-4897(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    13. "Differential regulation of urease activity in Helicobacter hepaticus and Helicobacter pylori."
      Belzer C., Stoof J., Beckwith C.S., Kuipers E.J., Kusters J.G., van Vliet A.H.M.
      Microbiology 151:3989-3995(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    14. "Supramolecular assembly and acid resistance of Helicobacter pylori urease."
      Ha N.-C., Oh S.-T., Sung J.Y., Cha K.A., Lee M.H., Oh B.-H.
      Nat. Struct. Biol. 8:505-509(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH NICKEL IONS, SUBUNIT STRUCTURE, CARBAMYLATION AT LYS-219.

    Entry informationi

    Entry nameiURE1_HELPY
    AccessioniPrimary (citable) accession number: P69996
    Secondary accession number(s): P14917, Q9R3B3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 4, 2005
    Last sequence update: January 4, 2005
    Last modified: October 1, 2014
    This is version 82 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The novel dodecameric structure of the enzyme may allow it to remain active at the cell surface at acidic gastric pH. Within this dodecameric structure the 12 active sites are clustered within the interior of the proteinaceous shell. This may allow a high local concentration of ammonia within the enzyme which may protect the nickel-chelating groups from protonation.

    Caution

    The orthologous protein is known as the alpha subunit (UreC) in most other bacteria.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Helicobacter pylori
      Helicobacter pylori (strain 26695): entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3