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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-Experimental evidence at protein leveli

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

Catalytic activityi

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.1 Publication

Enzyme 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

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 YwaC (ywaC), GTP pyrophosphokinase (relA), GTP pyrophosphokinase YjbM (yjbM)
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei44 – 441Allosteric pppGpp; from the opposite subunit1 Publication
Binding sitei52 – 521ATP (substrate)1 Publication
Metal bindingi72 – 721Magnesium1 Publication
Binding sitei72 – 721ATP (substrate)1 Publication
Binding sitei77 – 771ATP (substrate)1 Publication
Active sitei139 – 1391Possible proton acceptor1 Publication
Binding sitei148 – 1481Allosteric pppGpp; from the opposite subunit1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi21 – 288Allosteric pppGpp; by both subunits1 Publication
Nucleotide bindingi41 – 422Allosteric pppGpp; from this subunit1 Publication
Nucleotide bindingi46 – 483ATP (substrate)1 Publication
Nucleotide bindingi56 – 594ATP (substrate)1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, GTP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU11600-MONOMER.
UniPathwayiUPA00908; UER00884.

Names & Taxonomyi

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
Gene namesi
Name:yjbM
Ordered Locus Names:BSU11600
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi25 – 251K → A: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 1 Publication
Mutagenesisi42 – 421F → A: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 1 Publication
Mutagenesisi46 – 461R → G: Loss of (p)ppGpp synthesis, protein still forms tetramers. 1 Publication
Mutagenesisi139 – 1391E → V: Loss of (p)ppGpp synthesis, protein still forms tetramers. 1 Publication
Mutagenesisi148 – 1481N → G: No stimulation of (p)ppGpp stimulation by (p)ppGpp, protein still forms tetramers. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 211211GTP pyrophosphokinase YjbMPRO_0000390876Add
BLAST

Proteomic databases

PaxDbiO31611.

Expressioni

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 innoculation, decreasing until 3.5 hours as cells enter stationary phase (at protein level) (PubMed:22950019).2 Publications

Interactioni

Subunit structurei

Homotetramer (PubMed:26460002).1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100006416.

Structurei

Secondary structure

1
211
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 3128Combined sources
Beta strandi42 – 476Combined sources
Helixi50 – 5910Combined sources
Helixi64 – 696Combined sources
Beta strandi73 – 8210Combined sources
Helixi83 – 9513Combined sources
Beta strandi97 – 10711Combined sources
Helixi108 – 1136Combined sources
Beta strandi119 – 12911Combined sources
Beta strandi132 – 14413Combined sources
Helixi145 – 16016Combined sources
Turni161 – 1633Combined sources
Helixi167 – 19529Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO31611.
SMRiO31611. Positions 4-203.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RelA/SpoT family.Curated

Phylogenomic databases

eggNOGiCOG2357. LUCA.
HOGENOMiHOG000263233.
InParanoidiO31611.
KOiK07816.
OMAiHEEMYDI.
PhylomeDBiO31611.

Family and domain databases

InterProiIPR007685. RelA_SpoT.
[Graphical view]
PfamiPF04607. RelA_SpoT. 1 hit.
[Graphical view]
SMARTiSM00954. RelA_SpoT. 1 hit.
[Graphical view]

Sequencei

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
Checksum:i8FB2A73CE865FAA2
GO

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.

Genome annotation databases

EnsemblBacteriaiCAB13017; CAB13017; BSU11600.
GeneIDi939809.
KEGGibsu:BSU11600.
PATRICi18974037. VBIBacSub10457_1212.

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:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO31611.
SMRiO31611. Positions 4-203.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100006416.

Proteomic databases

PaxDbiO31611.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13017; CAB13017; BSU11600.
GeneIDi939809.
KEGGibsu:BSU11600.
PATRICi18974037. VBIBacSub10457_1212.

Phylogenomic databases

eggNOGiCOG2357. LUCA.
HOGENOMiHOG000263233.
InParanoidiO31611.
KOiK07816.
OMAiHEEMYDI.
PhylomeDBiO31611.

Enzyme and pathway databases

UniPathwayiUPA00908; UER00884.
BioCyciBSUB:BSU11600-MONOMER.

Family and domain databases

InterProiIPR007685. RelA_SpoT.
[Graphical view]
PfamiPF04607. RelA_SpoT. 1 hit.
[Graphical view]
SMARTiSM00954. RelA_SpoT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYJBM_BACSU
AccessioniPrimary (citable) accession number: O31611
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 19, 2010
Last sequence update: January 1, 1998
Last modified: September 7, 2016
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.