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Entry version 118 (29 Sep 2021)
Sequence version 1 (01 Jan 1998)
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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:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity 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

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi106NickelCombined sources1 Publication1 Publication1
Metal bindingi106Zinc1 Publication1
Metal bindingi107Nickel2 Publications1
Metal bindingi142NickelCombined sources1 Publication1 Publication1
Metal bindingi142Zinc1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
HPY:HP0900-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Hydrogenase/urease maturation factor HypBCurated
Alternative name(s):
Hydrogenase/urease nickel incorporation protein HypBCurated
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:hypB
Ordered Locus Names:HP_0900
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri85962 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000429 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002014421 – 242Hydrogenase/urease maturation factor HypBAdd BLAST242

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
O25560

PRoteomics IDEntifications database

More...
PRIDEi
O25560

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>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

Database of interacting proteins

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DIPi
DIP-3235N

Protein interaction database and analysis system

More...
IntActi
O25560, 2 interactors

Molecular INTeraction database

More...
MINTi
O25560

STRING: functional protein association networks

More...
STRINGi
85962.C694_04620

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1242
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
O25560

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

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PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni48 – 211G-domainBy similarityAdd BLAST164

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>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

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0378, Bacteria

Identification of Orthologs from Complete Genome Data

More...
OMAi
ECHLDAH

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O25560

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05390, HypB, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.300, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003495, CobW/HypB/UreG_dom
IPR004392, Hyd_mat_HypB
IPR027417, P-loop_NTPase

The PANTHER Classification System

More...
PANTHERi
PTHR30134, PTHR30134, 1 hit

Pfam protein domain database

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Pfami
View protein in Pfam
PF02492, cobW, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF52540, SSF52540, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00073, hypB, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i7C505390FB5C0142
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AE000511 Genomic DNA Translation: AAD07946.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D64632

NCBI Reference Sequences

More...
RefSeqi
NP_207693.1, NC_000915.1
WP_000003622.1, NC_018939.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAD07946; AAD07946; HP_0900

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
hpy:HP0900

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|85962.47.peg.959

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

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

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LPSX-ray2.00A/B1-242[»]
SMRiO25560
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

DIPiDIP-3235N
IntActiO25560, 2 interactors
MINTiO25560
STRINGi85962.C694_04620

Proteomic databases

PaxDbiO25560
PRIDEiO25560

Genome annotation databases

EnsemblBacteriaiAAD07946; AAD07946; HP_0900
KEGGihpy:HP0900
PATRICifig|85962.47.peg.959

Phylogenomic databases

eggNOGiCOG0378, Bacteria
OMAiECHLDAH
PhylomeDBiO25560

Enzyme and pathway databases

BioCyciHPY:HP0900-MONOMER

Family and domain databases

CDDicd05390, HypB, 1 hit
Gene3Di3.40.50.300, 1 hit
InterProiView protein in InterPro
IPR003495, CobW/HypB/UreG_dom
IPR004392, Hyd_mat_HypB
IPR027417, P-loop_NTPase
PANTHERiPTHR30134, PTHR30134, 1 hit
PfamiView protein in Pfam
PF02492, cobW, 1 hit
SUPFAMiSSF52540, SSF52540, 1 hit
TIGRFAMsiTIGR00073, hypB, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHYPB_HELPY
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O25560
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: January 1, 1998
Last modified: September 29, 2021
This is version 118 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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