Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P69996 (URE1_HELPY) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Urease subunit beta

EC=3.5.1.5
Alternative name(s):
Urea amidohydrolase subunit beta
Gene names
Name:ureB
Synonyms:hpuB
Ordered Locus Names:HP_0072
OrganismHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]
Taxonomic identifier85962 [NCBI]
Taxonomic lineageBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

Protein attributes

Sequence length569 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach. Ref.10

Catalytic activity

Urea + H2O = CO2 + 2 NH3. Ref.4 Ref.5 Ref.9

Cofactor

Binds 2 nickel ions per subunit.

Pathway

Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. HAMAP-Rule MF_01953

Subunit structure

Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits. Four heterohexamers assemble to form a 16 nm dodecameric complex. Ref.14

Subcellular location

Cytoplasm. Note: Also associates with the outer membrane upon autolysis of neighboring bacteria. Ref.11

Induction

By nickel ions. Ref.12 Ref.13

Post-translational modification

Carbamylation allows a single lysine to coordinate two nickel ions. HAMAP-Rule MF_01953

Disruption phenotype

Cells do not express urease. Ref.8

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.

Sequence similarities

Belongs to the urease family.

Contains 1 urease domain.

Caution

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

Biophysicochemical properties

Kinetic parameters:

KM=0.48 mM for urea Ref.4 Ref.5

Vmax=1.1 mmol/min/mg enzyme

pH dependence:

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

Ontologies

Keywords
   Biological processVirulence
   Cellular componentCytoplasm
   LigandMetal-binding
Nickel
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processpathogenesis

Inferred from electronic annotation. Source: UniProtKB-KW

urea catabolic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionnickel cation binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

urease activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 569569Urease subunit beta HAMAP-Rule MF_01953
PRO_0000067533

Regions

Domain131 – 569439Urease

Sites

Active site3221Proton donor Probable
Metal binding1361Nickel 2
Metal binding1381Nickel 2
Metal binding2191Nickel 1; via carbamate group
Metal binding2191Nickel 2; via carbamate group
Metal binding2481Nickel 1
Metal binding2741Nickel 1
Metal binding3621Nickel 2
Binding site2211Substrate Probable

Amino acid modifications

Modified residue2191N6-carboxylysine HAMAP-Rule MF_01953

Experimental info

Sequence conflict101V → A in CAA34933. Ref.2
Sequence conflict191D → A Ref.2
Sequence conflict221R → C AA sequence Ref.4
Sequence conflict271D → C AA sequence Ref.4
Sequence conflict1041M → T in CAA34933. Ref.2
Sequence conflict1811W → F in CAA34933. Ref.2
Sequence conflict1931L → F in CAA34933. Ref.2
Sequence conflict2181F → L in CAA34933. Ref.2
Sequence conflict2731F → Y in CAA34933. Ref.2
Sequence conflict5401P → S in CAA34933. Ref.2
Sequence conflict554 – 56916SKPAN…LFSIF → LNQPIK in CAA34933. Ref.2

Secondary structure

....................................................................................................................... 569
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P69996 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: 4C8A6BC6C8295584

FASTA56961,684
        10         20         30         40         50         60 
MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT LREGMSQSNN 

        70         80         90        100        110        120 
PSKEELDLII TNALIVDYTG IYKADIGIKD GKIAGIGKGG NKDMQDGVKN NLSVGPATEA 

       130        140        150        160        170        180 
LAGEGLIVTA GGIDTHIHFI SPQQIPTAFA SGVTTMIGGG TGPADGTNAT TITPGRRNLK 

       190        200        210        220        230        240 
WMLRAAEEYS MNLGFLAKGN ASNDASLADQ IEAGAIGFKI HEDWGTTPSA INHALDVADK 

       250        260        270        280        290        300 
YDVQVAIHTD TLNEAGCVED TMAAIAGRTM HTFHTEGAGG GHAPDIIKVA GEHNILPAST 

       310        320        330        340        350        360 
NPTIPFTVNT EAEHMDMLMV CHHLDKSIKE DVQFADSRIR PQTIAAEDTL HDMGIFSITS 

       370        380        390        400        410        420 
SDSQAMGRVG EVITRTWQTA DKNKKEFGRL KEEKGDNDNF RIKRYLSKYT INPAIAHGIS 

       430        440        450        460        470        480 
EYVGSVEVGK VADLVLWSPA FFGVKPNMII KGGFIALSQM GDANASIPTP QPVYYREMFA 

       490        500        510        520        530        540 
HHGKAKYDAN ITFVSQAAYD KGIKEELGLE RQVLPVKNCR NITKKDMQFN DTTAHIEVNP 

       550        560 
ETYHVFVDGK EVTSKPANKV SLAQLFSIF 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of the gastric pathogen Helicobacter pylori."
Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. expand/collapse author list , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.
Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Web resources

Protein Spotlight

Going unnoticed - Issue 95 of June 2008

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M60398 Genomic DNA. Translation: AAA25021.1.
X17079 Genomic DNA. Translation: CAA34933.1.
AE000511 Genomic DNA. Translation: AAD07143.1.
M84338 Genomic DNA. No translation available.
PIRURKCBP. B38537.
RefSeqNP_206872.1. NC_000915.1.
YP_006933994.1. NC_018939.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1E9YX-ray3.00B1-569[»]
1E9ZX-ray3.00B1-569[»]
ProteinModelPortalP69996.
SMRP69996. Positions 1-569.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP69996. 11 interactions.
MINTMINT-1567059.
STRING85962.HP0072.

Protein family/group databases

MEROPSM38.982.

Proteomic databases

PRIDEP69996.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAD07143; AAD07143; HP_0072.
GeneID13869248.
899104.
KEGGheo:C694_00350.
hpy:HP0072.
PATRIC20591347. VBIHelPyl33062_0075.

Phylogenomic databases

KOK01428.
OMAIVDHWGI.
OrthoDBEOG6ND0GM.
ProtClustDBPRK13985.

Enzyme and pathway databases

BioCycHPY:HP0072-MONOMER.
UniPathwayUPA00258; UER00370.

Family and domain databases

Gene3D2.30.40.10. 1 hit.
HAMAPMF_01953. Urease_alpha.
InterProIPR006680. Amidohydro_1.
IPR011059. Metal-dep_hydrolase_composite.
IPR011612. Urease_alpha_N.
IPR005848. Urease_asu.
IPR017951. Urease_asu_c.
IPR017950. Urease_asu_CS.
[Graphical view]
PfamPF01979. Amidohydro_1. 1 hit.
PF00449. Urease_alpha. 1 hit.
[Graphical view]
PRINTSPR01752. UREASE.
SUPFAMSSF51338. SSF51338. 2 hits.
TIGRFAMsTIGR01792. urease_alph. 1 hit.
PROSITEPS01120. UREASE_1. 1 hit.
PS00145. UREASE_2. 1 hit.
PS51368. UREASE_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP69996.

Entry information

Entry nameURE1_HELPY
AccessionPrimary (citable) accession number: P69996
Secondary accession number(s): P14917, Q9R3B3
Entry history
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: April 16, 2014
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Protein Spotlight

Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Helicobacter pylori

Helicobacter pylori (strain 26695): entries and gene names