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P69996

- URE1_HELPY

UniProt

P69996 - URE1_HELPY

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Protein
Urease subunit beta
Gene
ureB, hpuB, HP_0072
Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 Publications

Cofactori

Binds 2 nickel ions per subunit.

Kineticsi

  1. KM=0.48 mM for urea2 Publications

Vmax=1.1 mmol/min/mg enzyme

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 – 2211Substrate Inferred
Metal bindingi248 – 2481Nickel 2; via pros nitrogen
Metal bindingi274 – 2741Nickel 2; via tele nitrogen
Active sitei322 – 3221Proton donor Inferred
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
Complete GO annotation...

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 beta (EC:3.5.1.5)
Alternative name(s):
Urea amidohydrolase subunit beta
Gene namesi
Name:ureB
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
Note: Also associates with the outer membrane upon autolysis of neighboring bacteria.1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

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 betaUniRule annotation
PRO_0000067533Add
BLAST

Amino acid modifications

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

Post-translational modificationi

Carbamylation allows a single lysine to coordinate two nickel ions.UniRule 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 Publication

Protein-protein interaction databases

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

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiP69996.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini131 – 569439Urease
Add
BLAST

Sequence similaritiesi

Belongs to the urease family.
Contains 1 urease domain.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 101V → A in CAA34933. 1 Publication
Sequence conflicti19 – 191D → A1 Publication
Sequence conflicti22 – 221R → C AA sequence 1 Publication
Sequence conflicti27 – 271D → C AA sequence 1 Publication
Sequence conflicti104 – 1041M → T in CAA34933. 1 Publication
Sequence conflicti181 – 1811W → F in CAA34933. 1 Publication
Sequence conflicti193 – 1931L → F in CAA34933. 1 Publication
Sequence conflicti218 – 2181F → L in CAA34933. 1 Publication
Sequence conflicti273 – 2731F → Y in CAA34933. 1 Publication
Sequence conflicti540 – 5401P → S in CAA34933. 1 Publication
Sequence conflicti554 – 56916SKPAN…LFSIF → LNQPIK in CAA34933. 1 Publication
Add
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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 81 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.

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

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