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P69996

- URE1_HELPY

UniProt

P69996 - URE1_HELPY

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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

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

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
IPR029754. Urease_Ni-bd.
[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

        10         20         30         40         50
MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT
60 70 80 90 100
LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIKD GKIAGIGKGG
110 120 130 140 150
NKDMQDGVKN NLSVGPATEA LAGEGLIVTA GGIDTHIHFI SPQQIPTAFA
160 170 180 190 200
SGVTTMIGGG TGPADGTNAT TITPGRRNLK WMLRAAEEYS MNLGFLAKGN
210 220 230 240 250
ASNDASLADQ IEAGAIGFKI HEDWGTTPSA INHALDVADK YDVQVAIHTD
260 270 280 290 300
TLNEAGCVED TMAAIAGRTM HTFHTEGAGG GHAPDIIKVA GEHNILPAST
310 320 330 340 350
NPTIPFTVNT EAEHMDMLMV CHHLDKSIKE DVQFADSRIR PQTIAAEDTL
360 370 380 390 400
HDMGIFSITS SDSQAMGRVG EVITRTWQTA DKNKKEFGRL KEEKGDNDNF
410 420 430 440 450
RIKRYLSKYT INPAIAHGIS EYVGSVEVGK VADLVLWSPA FFGVKPNMII
460 470 480 490 500
KGGFIALSQM GDANASIPTP QPVYYREMFA HHGKAKYDAN ITFVSQAAYD
510 520 530 540 550
KGIKEELGLE RQVLPVKNCR NITKKDMQFN DTTAHIEVNP ETYHVFVDGK
560
EVTSKPANKV SLAQLFSIF
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
IPR029754. Urease_Ni-bd.
[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: November 26, 2014
This is version 84 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