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Protein

Hydrogenase/urease maturation factor HypB

Gene

hypB

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. Is also required for maturation of urease (PubMed:11123699, PubMed:12533448). Exhibits a low intrinsic GTPase activity, which is essential for nickel insertion (PubMed:12533448, PubMed:21239585, PubMed:22179820, PubMed:24338018).2 Publications4 Publications

Enzyme regulationi

Metal coordination and the nucleotide-bound state of HypB directly influence each other (PubMed:24338018). Binding of nickel in the G-domain decreases GTPase activity and modulates the oligomeric state of the protein (PubMed:21239585, PubMed:24338018). Binding of zinc inhibits the GTPase activity (PubMed:21239585, PubMed:24338018). GTP and GDP modulate coordination, stoichiometry, and affinity of nickel, but not zinc (PubMed:24338018). Potassium increases the GTPase activity but has no effect on the other biochemical properties of the protein (PubMed:24338018).2 Publications

Kineticsi

kcat is 0.0006 sec(-1) for the apo form. kcat is 0.0016 sec(-1) in the presence of 20 µM Ni(II).1 Publication
  1. KM=0.05 mM for GTP (apo form)1 Publication
  2. KM=0.16 mM for GTP (in the presence of 20 µM Ni(II))1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi106Nickel or zinc1 Publication1 Publication1
    Metal bindingi107Nickel or zinc1 Publication1
    Metal bindingi142Nickel or zinc1 Publication1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase
    LigandGTP-binding, Metal-binding, Nickel, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciHPY:HP0900-MONOMER

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Hydrogenase/urease maturation factor HypBCurated
    Alternative name(s):
    Hydrogenase/urease nickel incorporation protein HypBCurated
    Gene namesi
    Name:hypB
    Ordered Locus Names:HP_0900
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    Proteomesi
    • UP000000429 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Mutant has negligible hydrogenase activity and is severely impaired in urease activity.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi18K → A: Decreases interaction with HypA. 1 Publication1
    Mutagenesisi20V → A: Decreases interaction with HypA. 1 Publication1
    Mutagenesisi21K → A: Does not affect interaction with HypA. 1 Publication1
    Mutagenesisi22I → A: Decreases interaction with HypA. 1 Publication1
    Mutagenesisi59K → A: No hydrogenase activity, 1% urease activity. Normal amounts of apo-urease and HypB protein are produced. Hydrogenase activity is partially restored and urease activity is fully restored by growth on 5 uM Ni(2+). Almost loss of GTPase activity. 2 Publications1
    Mutagenesisi106 – 107CH → AA: Abrogates nickel binding and weakens the affinity for zinc. Cannot dimerize in the presence of nickel. 1 Publication2
    Mutagenesisi107H → A: Strong decrease in nickel affinity in the absence of nucleotide. 1 Publication1
    Mutagenesisi142C → S: Weakens metal binding and decouples the GTPase and metal binding activities. 1 Publication1
    Mutagenesisi168K → A: Abolishes GTP-dependent dimerization, but does not affect nickel-dependent dimerization. Loss of GTPase activity. 1 Publication1
    Mutagenesisi186M → L: Strong decrease in GTP-dependent dimerization, but does not affect nickel-dependent dimerization; when associated with V-190. 1 Publication1
    Mutagenesisi190F → V: Strong decrease in GTP-dependent dimerization, but does not affect nickel-dependent dimerization; when associated with L-186. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002014421 – 242Hydrogenase/urease maturation factor HypBAdd BLAST242

    Proteomic databases

    PaxDbiO25560

    Interactioni

    Subunit structurei

    Monomer and homodimer (PubMed:12533448, PubMed:24338018, PubMed:21239585, PubMed:22179820). Dimerization is induced by nickel, but not by zinc (PubMed:21239585). Dimerization is also induced by GTP (PubMed:22179820). Forms complexes with HypA (PubMed:12533448, PubMed:22179820).4 Publications

    Protein-protein interaction databases

    DIPiDIP-3235N
    IntActiO25560, 2 interactors
    MINTiO25560
    STRINGi85962.HP0900

    Structurei

    Secondary structure

    1242
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi29 – 43Combined sources15
    Beta strandi47 – 52Combined sources6
    Helixi59 – 66Combined sources8
    Beta strandi74 – 82Combined sources9
    Helixi85 – 91Combined sources7
    Turni92 – 94Combined sources3
    Beta strandi97 – 101Combined sources5
    Helixi110 – 122Combined sources13
    Turni123 – 128Combined sources6
    Beta strandi130 – 135Combined sources6
    Helixi142 – 145Combined sources4
    Beta strandi151 – 158Combined sources8
    Helixi159 – 161Combined sources3
    Helixi165 – 168Combined sources4
    Helixi170 – 174Combined sources5
    Beta strandi177 – 182Combined sources6
    Helixi184 – 186Combined sources3
    Turni187 – 191Combined sources5
    Helixi194 – 204Combined sources11
    Beta strandi210 – 212Combined sources3
    Helixi218 – 234Combined sources17

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4LPSX-ray2.00A/B1-242[»]
    ProteinModelPortaliO25560
    SMRiO25560
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni48 – 211G-domainBy similarityAdd BLAST164

    Domaini

    Contains a metal-binding site, which can bind nickel or zinc, with a higher affinity for zinc (PubMed:21239585). His-107 is an essential nickel ligand only in the nucleotide-free state of the protein (PubMed:24338018).2 Publications

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105E8T Bacteria
    COG0378 LUCA
    KOiK04652
    OMAiECHLDAH

    Family and domain databases

    InterProiView protein in InterPro
    IPR003495 CobW/HypB/UreG_dom
    IPR004392 Hyd_mat_HypB
    IPR012202 NiFe-hyd/urease_mat_GTPase
    IPR027417 P-loop_NTPase
    PANTHERiPTHR30134:SF2 PTHR30134:SF2, 1 hit
    PfamiView protein in Pfam
    PF02492 cobW, 1 hit
    PIRSFiPIRSF005624 Ni-bind_GTPase, 1 hit
    SUPFAMiSSF52540 SSF52540, 1 hit
    TIGRFAMsiTIGR00073 hypB, 1 hit

    Sequencei

    Sequence statusi: Complete.

    O25560-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSEQRQESLQ NNPNLSKKDV KIVEKILSKN DIKAAEMKER YLKEGLYVLN
    60 70 80 90 100
    FMSSPGSGKT TMLENLADFK DFKFCVVEGD LQTNRDADRL RKKGVSAHQI
    110 120 130 140 150
    TTGEACHLEA SMIEGAFDLL KDEGALEKSD FLIIENVGNL VCPSSYNLGA
    160 170 180 190 200
    AMNIVLLSVP EGDDKVLKYP TMFMCADAVI ISKADMVEVF NFRVSQVKED
    210 220 230 240
    MQKLKPEAPI FLMSSKDPKS LEDFKNFLLE KKRENYQSTH SF
    Length:242
    Mass (Da):27,310
    Last modified:January 1, 1998 - v1
    Checksum:i7C505390FB5C0142
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000511 Genomic DNA Translation: AAD07946.1
    PIRiD64632
    RefSeqiNP_207693.1, NC_000915.1
    WP_000003622.1, NC_018939.1

    Genome annotation databases

    EnsemblBacteriaiAAD07946; AAD07946; HP_0900
    GeneIDi899430
    KEGGiheo:C694_04620
    hpy:HP0900
    PATRICifig|85962.47.peg.959

    Similar proteinsi

    Entry informationi

    Entry nameiHYPB_HELPY
    AccessioniPrimary (citable) accession number: O25560
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
    Last sequence update: January 1, 1998
    Last modified: April 25, 2018
    This is version 105 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Helicobacter pylori
      Helicobacter pylori (strain 26695): entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

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