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Protein

Ribose-phosphate pyrophosphokinase

Gene

prs

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P).UniRule annotation1 Publication4 Publications

Miscellaneous

This enzyme uses a steady state ordered mechanism, where Mg2+ binds first, followed by Mg-ATP and lastly, ribose 5-phosphate.1 Publication

Catalytic activityi

ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate.UniRule annotation2 Publications

Cofactori

Mg2+1 PublicationUniRule annotation1 PublicationNote: Binds 2 Mg2+ ions per subunit. Each Mg2+ binds only one residue (His-136 and Asp-175, respectively) of this protein, however the magnesium ions also bind substrates and water molecules to complete their coordination spheres (PubMed:2169413, PubMed:11790837). Can also use Mn2+ and Cd2+ ions, but the activity is less than that obtained with Mg2+ ions (PubMed:2169413, PubMed:11790837).1 Publication2 Publications

Enzyme regulationi

Activated by inorganic phosphate, and to a lesser extent by sulfate ions (PubMed:2169413). In addition to form a complex with ATP, Mg2+ also acts as a cofactor (PubMed:2169413). Strongly inhibited by ADP through competitive binding at the activation site and at a specific allosteric site (PubMed:2169413, PubMed:16008562). Less strongly inhibited by alpha,beta-methylene ATP (mADP), AMP, GDP, GMP and UTP (PubMed:2169413, PubMed:16008562).2 Publications

Kineticsi

  1. KM=191 µM for ATP (at pH 8 and 37 degrees Celsius)1 Publication
  2. KM=230 µM for Rib-5-P (at pH 8 and 37 degrees Celsius)1 Publication
  3. KM=480 µM for Rib-5-P (at pH 8.2 and 37 degrees Celsius)1 Publication
  4. KM=660 µM for ATP (at pH 8.2 and 37 degrees Celsius)1 Publication
  1. Vmax=108 µmol/min/mg enzyme (at pH 8 and 37 degrees Celsius)1 Publication
  2. Vmax=250 µmol/min/mg enzyme (at pH 8.2 and 37 degrees Celsius)1 Publication

pH dependencei

Optimum pH is 8-8.5. Activities at pH 7 and pH 9.5 are 35% and 85% of the maximal activity, respectively.1 Publication

Pathwayi: 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route I).UniRule annotation2 Publications
Proteins known to be involved in this subpathway in this organism are:
  1. Ribose-phosphate pyrophosphokinase (prs)
This subpathway is part of the pathway 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route I), the pathway 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis and in Metabolic intermediate biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei106Allosteric inhibitorCombined sources1 Publication1
Binding sitei110Allosteric inhibitorCombined sources2 Publications1
Metal bindingi136Magnesium 11 PublicationUniRule annotationCombined sources1 Publication1
Binding sitei141Allosteric inhibitorCombined sources1 Publication1
Metal bindingi175Magnesium 21 PublicationUniRule annotationCombined sources1 Publication1
Active sitei1981 Publication1 Publication1
Binding sitei200Ribose-5-phosphateUniRule annotationBy similarity1
Binding sitei224Ribose-5-phosphateUniRule annotationBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi43 – 45ATPUniRule annotation1 Publication3
Nucleotide bindingi102 – 103ATPUniRule annotationCombined sources1 Publication1 Publication2

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAllosteric enzyme, Kinase, Transferase
Biological processNucleotide biosynthesis
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU00510-MONOMER
SABIO-RKP14193
UniPathwayiUPA00087; UER00172

Names & Taxonomyi

Protein namesi
Recommended name:
Ribose-phosphate pyrophosphokinase1 PublicationUniRule annotation (EC:2.7.6.1UniRule annotation2 Publications)
Short name:
RPPK1 PublicationUniRule annotation
Alternative name(s):
5-phospho-D-ribosyl alpha-1-diphosphate1 PublicationUniRule annotation
Phosphoribosyl diphosphate synthase1 PublicationUniRule annotation
Phosphoribosyl pyrophosphate synthase1 PublicationUniRule annotation
Short name:
P-Rib-PP synthase1 PublicationUniRule annotation
Short name:
PPRibP synthase1 Publication
Short name:
PRPP synthase1 PublicationUniRule annotation
Short name:
PRPPase1 PublicationUniRule annotation
Gene namesi
Name:prs1 PublicationUniRule annotation
Ordered Locus Names:BSU00510
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi198K → A: Strong decrease of the Vmax value compared to that of the wild-type. The affinity binding for ATP and Rib-5-P are slightly altered compared to the wild-type. The cooperativity of ADP binding is reduced. 1 Publication1
Mutagenesisi200R → A: Strong decrease of the Vmax value compared to that of the wild-type enzyme. The affinity binding for ATP and Rib-5-P are slightly altered compared to the wild-type. 1 Publication1
Mutagenesisi202R → A: 3-fold decrease in the affinity binding for ATP. Slight decrease of the Vmax value. 1 Publication1
Mutagenesisi204N → A: 4.5-fold decrease in the affinity binding for ATP. Slight decrease of the Vmax value. 1 Publication1
Mutagenesisi207E → A: 2.5-fold decrease in the affinity binding for ATP. Slight decrease of the Vmax value. 1 Publication1

Chemistry databases

DrugBankiDB02798 Alpha-Methylene Adenosine Monophosphate
DB03148 Phosphomethylphosphonic Acid Adenosyl Ester

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001411102 – 317Ribose-phosphate pyrophosphokinaseAdd BLAST316

Proteomic databases

PaxDbiP14193
PRIDEiP14193

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.1 Publication2 Publications

Protein-protein interaction databases

IntActiP14193, 2 interactors
MINTiP14193
STRINGi224308.Bsubs1_010100000260

Structurei

Secondary structure

1317
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 14Combined sources5
Helixi19 – 29Combined sources11
Beta strandi36 – 40Combined sources5
Beta strandi42 – 44Combined sources3
Beta strandi46 – 50Combined sources5
Beta strandi58 – 62Combined sources5
Helixi69 – 85Combined sources17
Beta strandi89 – 97Combined sources9
Turni99 – 102Combined sources4
Helixi114 – 125Combined sources12
Beta strandi129 – 134Combined sources6
Helixi138 – 143Combined sources6
Beta strandi148 – 151Combined sources4
Helixi154 – 162Combined sources9
Turni163 – 165Combined sources3
Beta strandi168 – 175Combined sources8
Helixi176 – 178Combined sources3
Helixi179 – 188Combined sources10
Beta strandi193 – 197Combined sources5
Beta strandi210 – 213Combined sources4
Beta strandi219 – 223Combined sources5
Beta strandi225 – 229Combined sources5
Helixi231 – 242Combined sources12
Beta strandi246 – 251Combined sources6
Beta strandi253 – 255Combined sources3
Helixi261 – 266Combined sources6
Beta strandi268 – 276Combined sources9
Beta strandi288 – 293Combined sources6
Helixi296 – 308Combined sources13
Helixi313 – 315Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DKRX-ray2.30A/B1-317[»]
1DKUX-ray2.20A/B1-317[»]
1IBSX-ray2.80A/B1-317[»]
ProteinModelPortaliP14193
SMRiP14193
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14193

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni149 – 150Allosteric inhibitor bindingCombined sources1 Publication2
Regioni228 – 232Ribose-5-phosphate bindingUniRule annotationCombined sources2 Publications5

Sequence similaritiesi

Belongs to the ribose-phosphate pyrophosphokinase family. Class I subfamily.1 PublicationUniRule annotation

Phylogenomic databases

eggNOGiENOG4105C5T Bacteria
COG0462 LUCA
HOGENOMiHOG000210451
InParanoidiP14193
KOiK00948
OMAiFGWARQD
PhylomeDBiP14193

Family and domain databases

CDDicd06223 PRTases_typeI, 1 hit
HAMAPiMF_00583_B RibP_PPkinase_B, 1 hit
InterProiView protein in InterPro
IPR000842 PRib_PP_synth_CS
IPR029099 Pribosyltran_N
IPR000836 PRibTrfase_dom
IPR029057 PRTase-like
IPR005946 Rib-P_diPkinase
IPR037515 Rib-P_diPkinase_bac
PfamiView protein in Pfam
PF14572 Pribosyl_synth, 1 hit
PF13793 Pribosyltran_N, 1 hit
SUPFAMiSSF53271 SSF53271, 1 hit
TIGRFAMsiTIGR01251 ribP_PPkin, 1 hit
PROSITEiView protein in PROSITE
PS00114 PRPP_SYNTHASE, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P14193-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNQYGDKNL KIFSLNSNPE LAKEIADIVG VQLGKCSVTR FSDGEVQINI
60 70 80 90 100
EESIRGCDCY IIQSTSDPVN EHIMELLIMV DALKRASAKT INIVIPYYGY
110 120 130 140 150
ARQDRKARSR EPITAKLFAN LLETAGATRV IALDLHAPQI QGFFDIPIDH
160 170 180 190 200
LMGVPILGEY FEGKNLEDIV IVSPDHGGVT RARKLADRLK APIAIIDKRR
210 220 230 240 250
PRPNVAEVMN IVGNIEGKTA ILIDDIIDTA GTITLAANAL VENGAKEVYA
260 270 280 290 300
CCTHPVLSGP AVERINNSTI KELVVTNSIK LPEEKKIERF KQLSVGPLLA
310
EAIIRVHEQQ SVSYLFS
Length:317
Mass (Da):34,868
Last modified:January 1, 1990 - v1
Checksum:i0D37FC81668111EB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X16518 Genomic DNA Translation: CAA34523.1
D26185 Genomic DNA Translation: BAA05286.1
AL009126 Genomic DNA Translation: CAB11827.1
PIRiS05372 KIBSRS
RefSeqiNP_387932.1, NC_000964.3
WP_003218353.1, NZ_JNCM01000028.1

Genome annotation databases

EnsemblBacteriaiCAB11827; CAB11827; BSU00510
GeneIDi936985
KEGGibsu:BSU00510
PATRICifig|224308.179.peg.51

Entry informationi

Entry nameiKPRS_BACSU
AccessioniPrimary (citable) accession number: P14193
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: May 23, 2018
This is version 145 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, Direct protein sequencing, Reference proteome

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