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Entry version 92 (08 May 2019)
Sequence version 1 (01 Jan 1998)
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Protein

GTP pyrophosphokinase YjbM

Gene

yjbM

Organism
Bacillus subtilis (strain 168)
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

Functions as a (p)ppGpp synthase; GDP can be used instead of GTP, resulting in an increase of (p)ppGpp synthesis (PubMed:18067544). The enzyme binds ATP, then GDP or GTP and catalysis is highly cooperative (PubMed:26460002). In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. Probably has a minor role in the stringent response (PubMed:18067544).2 Publications

Miscellaneous

The synthase activity of YjbM is greater than that of YwaC (PubMed:18067544).1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

Allosterically regulated by its own products; pppGpp simulates synthesis 10-fold more than ppGpp. 2 pppGpp molecules bind in a regulatory cleft in the middle of the tetramer in an asymmetric manner. There is a specific contact of Lys-25 to the gamma-phosphate of pppGpp, explaining why pppGpp stimulates activity but ppGpp does not (PubMed:26460002).1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: ppGpp biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes ppGpp from GTP.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GTP pyrophosphokinase (relA), GTP pyrophosphokinase YjbM (yjbM), GTP pyrophosphokinase YwaC (ywaC)
  2. no protein annotated in this organism
This subpathway is part of the pathway ppGpp biosynthesis, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes ppGpp from GTP, the pathway ppGpp biosynthesis and in Purine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei44Allosteric pppGpp; from the opposite subunit1 Publication1
Binding sitei52ATP (substrate)1 Publication1
<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 bindingi72Magnesium1 Publication1
Binding sitei72ATP (substrate)1 Publication1
Binding sitei77ATP (substrate)1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei139Possible proton acceptor1 Publication1
Binding sitei148Allosteric pppGpp; from the opposite subunit1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi21 – 28Allosteric pppGpp; by both subunits1 Publication8
Nucleotide bindingi41 – 42Allosteric pppGpp; from this subunit1 Publication2
Nucleotide bindingi46 – 48ATP (substrate)1 Publication3
Nucleotide bindingi56 – 59ATP (substrate)1 Publication4

<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 functionKinase, Transferase
LigandATP-binding, GTP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU11600-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00908;UER00884

<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:
GTP pyrophosphokinase YjbM (EC:2.7.6.51 Publication)
Alternative name(s):
(p)ppGpp synthase YjbM
Small alarmone synthase 11 Publication
Short name:
SAS 11 Publication
<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:yjbM
Ordered Locus Names:BSU11600
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<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
  • UP000001570 <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

No visible phenotype, double yjbM-ywaC and triple relA-yjbM-ywaC mutants are also viable (PubMed:18067544).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>Mutagenesisi25K → A: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 1 Publication1
Mutagenesisi42F → A: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 1 Publication1
Mutagenesisi46R → G: Loss of (p)ppGpp synthesis, protein still forms tetramers. 1 Publication1
Mutagenesisi139E → V: Loss of (p)ppGpp synthesis, protein still forms tetramers. 1 Publication1
Mutagenesisi148N → G: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003908761 – 211GTP pyrophosphokinase YjbMAdd BLAST211

Proteomic databases

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

More...
PaxDbi
O31611

PRoteomics IDEntifications database

More...
PRIDEi
O31611

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Expressed during exponential growth through the transition to the stationary phase, but not during entry of cells into stationary phase (PubMed:18067544). Protein continuously expressed with a peak at 2 hours after inoculation, decreasing until 3.5 hours as cells enter stationary phase (at protein level) (PubMed:22950019).2 Publications

<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

Homotetramer (PubMed:26460002).

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU11600

<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

1211
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
O31611

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
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

<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

Belongs to the RelA/SpoT family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG2357 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000263233

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O31611

KEGG Orthology (KO)

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KOi
K07816

Identification of Orthologs from Complete Genome Data

More...
OMAi
VWATIEH

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O31611

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05399 NT_Rel-Spo_like, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR007685 RelA_SpoT

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04607 RelA_SpoT, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00954 RelA_SpoT, 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.

O31611-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDDKQWERFL VPYRQAVEEL KVKLKGIRTL YEYEDDHSPI EFVTGRVKPV
60 70 80 90 100
ASILEKARRK SIPLHEIETM QDIAGLRIMC QFVDDIQIVK EMLFARKDFT
110 120 130 140 150
VVDQRDYIAE HKESGYRSYH LVVLYPLQTV SGEKHVLVEI QIRTLAMNFW
160 170 180 190 200
ATIEHSLNYK YSGNIPEKVK LRLQRASEAA SRLDEEMSEI RGEVQEAQAA
210
FSRKKKGSEQ Q
Length:211
Mass (Da):24,704
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:i8FB2A73CE865FAA2
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AL009126 Genomic DNA Translation: CAB13017.1

Protein sequence database of the Protein Information Resource

More...
PIRi
E69844

NCBI Reference Sequences

More...
RefSeqi
NP_389042.1, NC_000964.3
WP_003245294.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB13017; CAB13017; BSU11600

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
939809

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU11600

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.1249

<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
AL009126 Genomic DNA Translation: CAB13017.1
PIRiE69844
RefSeqiNP_389042.1, NC_000964.3
WP_003245294.1, NZ_JNCM01000035.1

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
5DECX-ray2.00A/B/C/D2-211[»]
5DEDX-ray2.94A/B/C/D/E/F/G/H2-211[»]
5F2VX-ray2.80O/P/Q/R/S/T/U/V/W/X/Y/Z3-211[»]
SMRiO31611
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU11600

Proteomic databases

PaxDbiO31611
PRIDEiO31611

Genome annotation databases

EnsemblBacteriaiCAB13017; CAB13017; BSU11600
GeneIDi939809
KEGGibsu:BSU11600
PATRICifig|224308.179.peg.1249

Phylogenomic databases

eggNOGiCOG2357 LUCA
HOGENOMiHOG000263233
InParanoidiO31611
KOiK07816
OMAiVWATIEH
PhylomeDBiO31611

Enzyme and pathway databases

UniPathwayiUPA00908;UER00884
BioCyciBSUB:BSU11600-MONOMER

Family and domain databases

CDDicd05399 NT_Rel-Spo_like, 1 hit
InterProiView protein in InterPro
IPR007685 RelA_SpoT
PfamiView protein in Pfam
PF04607 RelA_SpoT, 1 hit
SMARTiView protein in SMART
SM00954 RelA_SpoT, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiYJBM_BACSU
<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: O31611
<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: January 19, 2010
Last sequence update: January 1, 1998
Last modified: May 8, 2019
This is version 92 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, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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